My protein has 4 NAG and 1 ALS residue in its sequence. When I tried to simulate the protein using gromos96 53 a6 force field , it's showing a fatal error as: residue 'ALS' not found in residue topology database.
How can I troubleshoot this problem? Can you tell me the steps to overcome this problem?
P.S- I have already gone through this website and tried to include the new residue in "residuetypes.dat" file, but the file was not saving the modified residue.
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Have you been through the following tutorial?
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg/o/gmx.pdf
It explains how to create topology of a drug using PRODRG.
Have you tried to save the file in your current working directory?
The link you quote is exactly what needs to be done. If the changes aren't saved, then you probably don't have permission to edit the files, but you can make a local copy of the force field and library files (e.g. residuetypes.dat) in your working directory and edit those.
it is basically the common point of Dr. Chaurasi and Dr. Lemkul's answers. Create a new topoly using PRODRG for gromacs and Add it to your local copy of amino acid topology file with the desired name with all the parameters required by gromacs.
You can also edit aminoacid.rtp file add a new residue. In case of NAG you may copy/paste the following sentences. Remember that I have corrected the sentences for bond and atom only and the reset sentence for [ angles ] [ impropers ] [ dihedrals ] remained to be corrected:
[ NAG ]
[ atoms ]
C1 CH1 0.40000 0
O5 OA -0.36000 0
C5 CH1 0.16000 0
C6 CH2 0.15000 1
O6 OA -0.54800 1
H6 H 0.39800 1
C2 CH1 0.15000 2
N2 N -0.28000 2
H2 H 0.39800 2
C3 CH1 0.15000 3
O3 OA -0.54800 3
H3 H 0.39800 3
C4 CH1 0.160 4
O4 OA -0.360 4
C7 C 0.27000 5
O7 O -0.380 5
C8 CH3 0.00000 6
[ bonds ]
C1 O5 gb_19
C1 C2 gb_25
O5 C5 gb_19
C5 C6 gb_25
C5 C4 gb_25
C6 O6 gb_19
O6 H6 gb_1
C2 O2 gb_19
C2 C3 gb_25
N2 C7 gb_20
C7 N2 gb_20
O7 C7 gb_19
C8 C7 gb_25
C3 O3 gb_19
C3 C4 gb_25
O3 H3 gb_1
C4 O4 gb_19
O4 +N gb_19
[ angles ]
; ai aj ak gromos type
-O C1 O5 ga_8
-O C1 C2 ga_8
O5 C1 C2 ga_8
C1 O5 C5 ga_9
O5 C5 C6 ga_8
O5 C5 C4 ga_8
C6 C5 C4 ga_7
C5 C6 O6 ga_8
C6 O6 H6 ga_11
C1 C2 O2 ga_8
C1 C2 C3 ga_7
O2 C2 C3 ga_8
C2 O2 H2 ga_11
C2 C3 O3 ga_8
C2 C3 C4 ga_7
O3 C3 C4 ga_8
C3 O3 H3 ga_11
C5 C4 C3 ga_7
C5 C4 O4 ga_8
C3 C4 O4 ga_8
C4 O4 +N ga_9
[ impropers ]
; ai aj ak al gromos type
C1 O5 -O C2 gi_2
C5 O5 C6 C4 gi_2
C2 O2 C3 C1 gi_2
C3 O3 C2 C4 gi_2
C4 C3 O4 C5 gi_2
[ dihedrals ]
; ai aj ak al gromos type
-C -O C1 C2 gd_14
-O C1 C2 C3 gd_17
-O C1 C2 C3 gd_7
O5 C1 C2 C3 gd_7
O5 C1 C2 O2 gd_8
-O C1 C2 O2 gd_8
C1 C2 O2 H2 gd_12
C1 C2 C3 C4 gd_17
C1 C2 C3 O3 gd_7
O2 C2 C3 C4 gd_7
O2 C2 C3 O3 gd_8
C2 C3 O3 H3 gd_12
C2 C3 C4 C5 gd_17
C2 C3 C4 O4 gd_7
O3 C3 C4 C5 gd_7
O3 C3 C4 O4 gd_8
C2 C1 O5 C5 gd_14
C1 O5 C5 C4 gd_14
C4 C5 C6 O6 gd_17
C4 C5 C6 O6 gd_7
O5 C5 C6 O6 gd_8
C5 C6 O6 H6 gd_12
C6 C5 C4 C3 gd_17
O5 C5 C4 C3 gd_7
C6 C5 C4 O4 gd_7
O5 C5 C4 O4 gd_8
C3 C4 O4 +N gd_14
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