How can I find which dssp version works with gromacs 5.0.2 version ?

03 March 2015 23 4K Report

I have installed gromacs 5.0.2 version and tried to perform secondary structure analysis ,but there was a fatal error showing use -ver option . i tried using the -ver 2 in the command line still its showing same error . Finally i installed dssp 2.0.4 version in usr/local/bin/dssp but still the error persists .

Abhishek Acharya

I have gromacs 5.0.4 with dssp 2.0.4. It works fine. Can you post the exact error you are getting. Maybe that could help.

Kesavan Ekambaram

Im using gromacs on my macbook pro this was the error after executing do_dssp command ..

Fatal error:

Failed to execute command: Try specifying your dssp version with the -ver option.

Abhishek Acharya

Try running dssp directly. See if it runs properly. If not, there may be a problem in your installation. If it works fine, could be a bug in gromacs. In that case report the problem to the gromacs developers, you might get a fix in the next release. I have no experience of using Gromacs on Mac OS, this is as much as I can help.

If the problem is in DSSP installation, you might want to have a look at this:

http://macosxpostdoc.blogspot.in/2012/09/two-for-price-of-one-mac-os-x-without.html

Aditya Kumar Sarkar

Dear Kesavan,

As far as I know this problem GROMACS have this compatibility issue for DSSP versions. At least in my case, Gromacs 4.5.5, I have faced the same problem. When I search in the internet I found that the do_dssp program of Gromacs4.5.5 have bug and people suggest to use some older version of Gromacs.

This link might help you:

http://comments.gmane.org/gmane.science.biology.gromacs.user/60781

Hope this help

Aditya

Erik Marklund

The problem was that dssp 2 is invoked in a different way than earlier versions, which caused do_dssp to choke. do_dssp was updated to handle the new dssp syntax in gromacs version 4.6 (http://redmine.gromacs.org/issues/891).

You say that you set an environment variable to point to the dssp executable in usr/local/bin/dssp, but if that is really the path you give then that's your problem. It should have a leading '/'.

Erik Marklund

Was that the problem?

If not, could it be that you need to set the permissions on dssp such that it is executable. The freshly downloaded file is not executable on unix-like systems, so you need to do chmod u+x dssp or similar. If you don't it will yield exactly the error message you reported.

Kesavan Ekambaram

I have tried using the permission for running dssp but still same error exists for me . i still dont know how to solve out this problem..?

Erik Marklund

Hm. I just tried a fresh install of gromacs 5.0.4 and dssp 2.0.4. Worked like a charm.

Can you give the EXACT commands you issued (copied from terminal to avoid typos), including the definition of environment variables?

Kesavan Ekambaram

Thank you for your kind help sir, i have also tried the same by changing the gromacs version to 5.0.4 . But i dint set the env for DSSP . so could you please help me with the commands that you followed to install dssp in gromacs 5.0.4 version

Erik Marklund

Assuming you put the dssp executable in /home/myname/bin, and that you are using bash, you do the following:

export DSSP=/home/myname/bin/dssp

The run do_dssp -s ... -f ... and you should get the secondary structure content.

(EDIT: If you use csh or tsch, you would not use export, but rather setenv DSSP /home/myname/bin/dssp)

Kesavan Ekambaram

thank you sir , now DSSP is working perfectly without any error for me in gromacs 5.0.4 version . thank you for kindly helping me to solve out this problem

Ibrahim Issah

you can also use rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/ in your terminal to get the file but please don't forget to use the path that gromacs can recognize. (/usr/local/bin/dssp) . thus rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /usr/local/bin/dssp. and if you are getting permission denied error message. begin with the sudo command : like sudo rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /usr/local/bin/dssp

Leila Karami

Dear Erik,

I have a problem same as Kesavan Ekambaram in Gromacs 5.1.3.

I located dssp in /usr/local/bin and I did following:

chmod +x dssp

export DSSP=/usr/local/bin/dssp

gmx_mpi do_dssp -s ... -f ...

But, again I encountered the previous fatal error:

Failed to execute command: Try specifying your dssp version with the -ver

option.

How to fix it?

Erik Marklund

Dear Leila,

Have you confirmed that your dssp is working? Try running dssp (not gmx do_dssp) on a pdb file.

Leila Karami

Yes,

cd /usr/local/bin

[rahban@ibbs bin]$ dssp

W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995

CMBI version by [email protected] / April 4, 2006

USAGE

dssp [Options] PDB_File DSSP_File -> Read PDB_File and write DSSP_File

dssp [Options] -- dssp_file -> Read from stdin and write DSSP_File

dssp -h -> Display this help screen

OPTIONS

-na Disables the calculation of accessible surface.

-c Classic (old) format.

-w Wide 2002 format (for future use,not the current standard).

-v Verbose.

-- Read from standard input.

-h -? Prints a help message.

-V Prints version, as in first line of the output.

ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS

By [email protected]

-ssa Adds information about disulfide bonds to output file

-x Renames residues with incomplete sidechains to 'X'

-alt2 Keeps an additional AltLoc indicator at the line ends

Leila Karami

[root@ibbs bin]# dssp 1JPO.pdb

==== Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ==== DATE=28-FEB-2017 .

REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 .

HEADER HYDROLASE 03-JUL-97 1JPO .

COMPND 2 MOLECULE: LYSOZYME; .

SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; .

AUTHOR G.M.BRADBROOK,J.R.HELLIWELL,J.HABASH .

!!! Residue LEU 129 A has 5 instead of expected 4 sidechain atoms.

last sidechain atom name is OXT

calculated solvent accessibility includes extra atoms !!!

129 1 4 4 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) .

6625.0 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) .

90 69.8 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES .

2 1.6 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .

11 8.5 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .

1 0.8 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES .

2 1.6 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES .

1 0.8 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES .

0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES .

0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES .

0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES .

0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES .

9 7.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES .

26 20.2 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES .

33 25.6 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES .

5 3.9 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES .

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** .

0 0 0 0 0 1 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 RESIDUES PER ALPHA HELIX .

1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER .

2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER .

0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET .

# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA

1 1 A K 0 0 93 0, 0.0 39,-2.6 0, 0.0 2,-0.6 0.000 360.0 360.0 360.0 155.6 35.9 21.1 -11.7

2 2 A V B -A 39 0A 97 37,-0.2 37,-0.2 38,-0.1 2,-0.1 -0.916 360.0-146.0-101.9 112.9 34.1 18.0 -10.4

3 3 A F - 0 0 16 35,-2.7 2,-0.3 -2,-0.6 3,-0.0 -0.457 10.6-123.7 -77.1 154.8 35.4 16.9 -7.0

4 4 A G > - 0 0 34 -2,-0.1 4,-2.5 1,-0.1 5,-0.2 -0.716 29.5-113.0 -92.5 149.0 35.6 13.4 -5.9

5 5 A R H > S+ 0 0 87 -2,-0.3 4,-2.0 1,-0.2 5,-0.1 0.902 116.8 40.1 -47.4 -54.3 33.8 12.7 -2.6

6 6 A a H > S+ 0 0 42 1,-0.2 4,-2.5 2,-0.2 -1,-0.2 0.864 112.6 56.7 -67.3 -34.3 37.0 12.0 -0.6

7 7 A E H > S+ 0 0 95 1,-0.2 4,-1.9 2,-0.2 -1,-0.2 0.888 110.6 44.5 -63.0 -40.4 38.8 14.8 -2.3

8 8 A L H X S+ 0 0 0 -4,-2.5 4,-3.0 2,-0.2 5,-0.3 0.872 108.8 56.8 -72.3 -37.9 36.2 17.2 -1.1

9 9 A A H X S+ 0 0 0 -4,-2.0 4,-2.2 -5,-0.2 -2,-0.2 0.961 109.8 45.6 -58.6 -47.4 36.1 15.7 2.4

10 10 A A H X S+ 0 0 44 -4,-2.5 4,-2.3 1,-0.2 -1,-0.2 0.912 113.5 48.9 -62.4 -45.7 39.8 16.4 2.7

11 11 A A H X S+ 0 0 5 -4,-1.9 4,-1.5 1,-0.2 -1,-0.2 0.929 112.9 46.4 -61.7 -46.4 39.5 20.0 1.3

12 12 A M H S+ 0 0 1 -4,-3.0 5,-2.1 1,-0.2 6,-0.3 0.854 111.3 52.9 -64.4 -36.0 36.6 20.9 3.6

13 13 A K H >> - 0 0 39 -2,-0.6 3,-2.5 -5,-0.3 4,-0.8 -0.287 30.9-101.5 -65.0 153.9 30.3 17.3 11.3

25 25 A L H 3> S+ 0 0 1 1,-0.3 4,-2.1 2,-0.2 5,-0.2 0.765 118.5 66.1 -42.8 -38.9 32.2 17.1 8.0

26 26 A G H 3> S+ 0 0 0 1,-0.2 4,-2.4 2,-0.2 -1,-0.3 0.832 96.0 56.2 -57.0 -35.3 29.7 14.5 6.7

27 27 A N H S+ 0 0 20 -3,-2.5 4,-2.6 1,-0.2 -1,-0.2 0.928 108.7 47.2 -62.2 -45.2 26.9 17.2 6.7

28 28 A W H X S+ 0 0 0 -4,-0.8 4,-2.2 -3,-0.2 -2,-0.2 0.880 113.3 45.8 -64.3 -44.2 29.0 19.4 4.5

29 29 A V H X S+ 0 0 0 -4,-2.1 4,-2.1 2,-0.2 -1,-0.2 0.907 113.8 50.5 -68.9 -36.4 30.0 16.7 1.9

30 30 A b H X S+ 0 0 0 -4,-2.4 4,-2.2 -5,-0.2 5,-0.2 0.937 108.9 51.4 -66.8 -44.5 26.4 15.6 1.8

31 31 A A H X S+ 0 0 0 -4,-2.6 4,-1.8 1,-0.2 5,-0.2 0.942 110.4 48.9 -58.1 -46.6 25.1 19.1 1.2

32 32 A A H X>S+ 0 0 0 -4,-2.2 4,-2.5 2,-0.2 6,-1.3 0.880 108.1 55.3 -61.1 -40.5 27.6 19.5 -1.7

33 33 A K H X5S+ 0 0 67 -4,-2.1 4,-1.3 4,-0.2 -1,-0.2 0.962 116.5 34.6 -57.8 -52.8 26.5 16.2 -3.2

34 34 A F H > -D 52 0C 28 -2,-0.4 4,-1.6 -7,-0.2 5,-0.8 -0.402 3.8-142.7 -66.3 141.7 22.2 32.4 -3.6

60 60 A S T 45S+ 0 0 0 -9,-1.7 13,-0.3 3,-0.2 6,-0.2 0.519 88.6 71.9 -82.4 -12.0 22.8 35.9 -5.0

61 61 A R T 45S+ 0 0 99 11,-0.2 12,-1.7 -10,-0.1 -1,-0.2 0.813 120.1 9.2 -75.7 -28.5 19.9 37.7 -3.3

62 62 A W T 45S+ 0 0 102 -3,-0.5 13,-2.6 10,-0.2 -2,-0.2 0.704 133.4 35.3-118.3 -32.1 21.5 37.6 0.1

63 63 A W T - 0 0 13 -9,-0.1 3,-1.4 1,-0.1 -2,-0.1 -0.882 68.8-124.9-103.8 117.9 19.6 40.3 -9.1

70 70 A P T 3 S+ 0 0 111 0, 0.0 2,-0.3 0, 0.0 -1,-0.1 0.706 92.7 5.7 -20.3 -86.0 16.7 42.7 -8.2

71 71 A G T 3 S+ 0 0 49 2,-0.0 2,-0.1 0, 0.0 -10,-0.0 -0.464 92.2 176.3-112.3 62.5 17.0 43.7 -4.5

72 72 A S < - 0 0 40 -3,-1.4 2,-0.3 -2,-0.3 -10,-0.2 -0.265 22.7-161.3 -74.2 152.9 20.3 42.0 -3.7

73 73 A R - 0 0 127 -12,-1.7 -9,-0.1 -13,-0.3 3,-0.1 -0.739 11.0-151.5-118.9 161.5 22.4 42.0 -0.6

74 74 A N > + 0 0 51 -2,-0.3 3,-1.4 -11,-0.1 -11,-0.2 -0.511 29.2 161.1-136.2 63.5 26.0 41.0 -0.6

75 75 A L T 3 S+ 0 0 85 -13,-2.6 -12,-0.2 1,-0.3 -11,-0.1 0.691 77.9 45.1 -62.6 -21.5 26.3 39.7 3.0

76 76 A d T 3 S- 0 0 8 -13,-2.2 -1,-0.3 2,-0.2 -12,-0.1 0.475 104.4-133.2 -98.3 -6.4 29.5 37.7 2.2

77 77 A N < + 0 0 132 -3,-1.4 -13,-0.1 -14,-0.3 -2,-0.1 0.896 64.2 116.3 54.0 53.3 31.0 40.7 0.4

78 78 A I S S- 0 0 45 -15,-0.5 -13,-2.0 16,-0.0 -1,-0.2 -0.969 70.4-107.4-148.4 146.0 32.1 38.7 -2.6

79 79 A P B > -e 65 0D 64 0, 0.0 3,-0.7 0, 0.0 4,-0.3 -0.587 30.8-124.8 -71.9 148.8 31.3 38.6 -6.3

80 80 A c G > S+ 0 0 1 -15,-2.5 3,-1.6 1,-0.2 4,-0.2 0.826 106.7 66.6 -66.2 -28.7 29.3 35.5 -7.3

81 81 A S G > S+ 0 0 86 -16,-0.4 3,-2.2 1,-0.3 -1,-0.2 0.858 90.4 63.3 -58.1 -38.3 31.9 34.6 -9.9

82 82 A A G X S+ 0 0 32 -3,-0.7 3,-0.6 1,-0.3 8,-0.3 0.662 94.9 61.7 -62.6 -15.8 34.5 33.9 -7.2

83 83 A L G < S+ 0 0 1 -3,-1.6 -28,-0.5 -4,-0.3 -1,-0.3 0.537 93.4 66.5 -87.3 -6.4 32.2 31.1 -6.0

84 84 A L G < S+ 0 0 44 -3,-2.2 -1,-0.2 -4,-0.2 -2,-0.2 0.179 79.0 108.5 -99.0 14.2 32.6 29.3 -9.3

85 85 A S S < S- 0 0 49 -3,-0.6 6,-0.1 2,-0.2 -3,-0.0 -0.457 78.4-117.3 -90.7 168.8 36.3 28.5 -9.0

86 86 A S S S+ 0 0 71 -2,-0.1 2,-0.9 1,-0.1 -1,-0.1 0.689 100.7 79.2 -72.2 -23.4 38.1 25.2 -8.5

87 87 A D S > S- 0 0 92 1,-0.1 3,-0.7 -47,-0.0 4,-0.3 -0.808 70.9-159.9 -89.9 106.1 39.5 26.6 -5.2

88 88 A I T 3> + 0 0 5 -2,-0.9 4,-2.8 1,-0.2 3,-0.4 0.503 62.2 104.2 -67.3 -5.2 36.6 26.2 -2.7

89 89 A T H 3> S+ 0 0 40 1,-0.2 4,-3.1 2,-0.2 5,-0.2 0.854 79.6 47.7 -44.5 -53.4 38.0 28.8 -0.2

90 90 A A H S+ 0 0 23 -3,-0.7 4,-1.9 -8,-0.3 -1,-0.2 0.903 114.7 47.2 -58.0 -43.3 35.6 31.7 -1.1

91 91 A S H > S+ 0 0 4 -3,-0.4 4,-2.9 -4,-0.3 -1,-0.2 0.898 114.0 47.8 -64.0 -43.7 32.6 29.3 -1.0

92 92 A V H X S+ 0 0 1 -4,-2.8 4,-2.1 2,-0.2 -2,-0.2 0.941 111.1 50.0 -63.3 -48.8 33.8 27.9 2.4

93 93 A N H X S+ 0 0 78 -4,-3.1 4,-0.7 -5,-0.2 -2,-0.2 0.855 115.6 43.1 -61.2 -35.3 34.4 31.4 3.9

94 94 A d H >X S+ 0 0 3 -4,-1.9 4,-2.1 -5,-0.2 3,-1.0 0.932 109.9 56.1 -76.0 -43.0 30.9 32.5 2.8

95 95 A A H 3X S+ 0 0 0 -4,-2.9 4,-2.5 1,-0.3 -2,-0.2 0.849 102.9 56.9 -56.2 -35.7 29.2 29.3 3.9

96 96 A K H 3X S+ 0 0 46 -4,-2.1 4,-0.6 1,-0.2 -1,-0.3 0.835 107.8 47.7 -64.5 -34.8 30.7 29.8 7.4

97 97 A K H < S+ 0 0 10 -4,-2.1 3,-1.8 1,-0.2 4,-0.4 0.937 108.2 51.8 -62.5 -46.1 25.6 31.8 6.3

99 99 A V H 3< S+ 0 0 2 -4,-2.5 5,-0.3 1,-0.3 3,-0.3 0.688 107.6 53.8 -67.0 -17.3 25.7 29.0 9.0

100 100 A S T 3< S+ 0 0 40 -4,-0.6 -1,-0.3 -3,-0.4 -2,-0.2 0.372 95.0 75.5 -96.2 2.7 26.3 31.6 11.7

101 101 A D S < S- 0 0 102 -3,-1.8 -1,-0.2 3,-0.2 -2,-0.2 0.649 110.6 -62.3 -92.8 -18.6 23.2 33.7 10.7

102 102 A G S S+ 0 0 68 -4,-0.4 2,-0.7 -3,-0.3 3,-0.1 -0.281 112.5 38.5 178.3 -88.6 20.2 31.8 11.9

103 103 A N S > S- 0 0 101 1,-0.2 3,-2.7 -5,-0.1 4,-0.3 -0.281 85.0-132.2 -92.4 51.1 18.8 28.3 11.1

104 104 A G G > S- 0 0 11 -2,-0.7 3,-0.5 -5,-0.3 -1,-0.2 -0.099 77.9 -12.9 41.7-121.4 22.2 26.5 10.8

105 105 A M G > S+ 0 0 0 1,-0.2 3,-2.3 2,-0.1 -1,-0.3 0.366 108.5 98.7 -92.1 6.1 22.4 24.4 7.7

106 106 A N G < + 0 0 54 -3,-2.7 -1,-0.2 1,-0.3 -2,-0.2 0.613 66.1 82.1 -66.4 -8.6 18.6 24.7 7.0

107 107 A A G < S+ 0 0 45 -3,-0.5 2,-0.7 -4,-0.3 -1,-0.3 0.740 82.3 66.7 -66.1 -23.8 19.9 27.4 4.6

108 108 A W S S- 0 0 8 -3,-2.3 4,-1.8 1,-0.2 3,-0.5 -0.887 71.5-162.8-103.5 108.5 20.6 24.6 2.2

109 109 A V H > S+ 0 0 66 -2,-0.7 4,-3.0 1,-0.2 5,-0.3 0.923 88.9 55.8 -54.9 -47.1 17.4 23.0 1.0

110 110 A A H >>S+ 0 0 14 1,-0.3 4,-2.8 2,-0.2 5,-0.5 0.823 107.6 50.0 -56.6 -35.8 19.1 19.9 -0.3

111 111 A W H >>S+ 0 0 13 -3,-0.5 5,-3.4 -6,-0.2 4,-1.5 0.893 111.0 48.5 -71.0 -41.2 20.6 19.3 3.1

112 112 A R H

Erik Marklund

That does not look like a recent dssp. At least it doesn't match mine:

>>>

mkdssp 2.2.1 options:

-h [ --help ] Display help message

-i [ --input ] arg Input file

-o [ --output ] arg Output file, use 'stdout' to output to screen

-v [ --verbose ] Verbose output

--version Print version

-d [ --debug ] arg Debug level (for even more verbose output)

Examples:

To calculate the secondary structure for the file 1crn.pdb and

write the result to a file called 1crn.dssp, you type:

mkdssp -i 1crn.pdb -o 1crn.dssp

Leila Karami

I got dssp file (dssp-2.0.4-linux-amd64) from ftp://ftp.cmbi.ru.nl/pub/software/dssp/, then I located it in /usr/local/bin and then I used chmod+x dssp.

After using mkdssp -i 1JPO.pdb -o 1JPO.dssp,

-bash: mkdssp: command not found

Erik Marklund

Not necessarily. But when you executed dssp earlier you used the dssp found by your system, which is not necessarily the one in /usr/local/bin. 'which dssp' will tell you the location of the dssp used. Alternatively, you can issue ./dssp in /usr/local/bin or provide the full path /usr/local/bin/dssp in order to make sure you use the intended executable.

It was suggested on the gromacs mailing list, just an hour ago, that mpi-enabled gromacs might be a bad choice for running analysis tools that in turn spawn new processes. Do you have a non-mpi version of gromacs that you could use instead? (hint: if not, install one).

Badges
Science topic

More Kesavan Ekambaram's questions See All

How to compute the evolution of local interactions in the particular regions of the protein ?

Dear All, I would like to study the evolution of local interactions in the particular regions of the protein over the dynamic trajectory. Could you please help me out with the suitable...

10 November 2018 2,385 3 View

How to find the dihedral angle of particular residue over the period of simulation time?

Dear Friends, I would like to perform the dihedral angle calculation of particular residue over the period of simulation time. Could you please help me out in creating the ndx file using make_ndx...

02 March 2018 6,275 3 View

How to perform the PIEDA calculation for the receptor-ligand residues using FMO ?

Dear All, Im trying to compute the PIEDA for the receptor-ligand residues using the FMO calculation. Could you help me in providing the steps to create the input put file for running the...

10 November 2017 3,557 2 View

How to calculate the host-guest binding affinity using quantum mechanics

05 June 2017 2,089 4 View

How to install ORCA in gromacs 4.6.5 ?

01 February 2016 5,724 2 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View