I am trying to run simulation of a glucosylated residue which covalently interact with aspartate. During validation of topology and preparation of energy minimization (EM) step (grompp) I am getting the following error:
NOTE 1 [file em.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 1782997164
WARNING 1 [file ffbonded.itp, line 1248]:
Overriding Bond parameters.
old: 0.149 209200 0.149 209200
new: C CT 1 0.1522 167360.0
WARNING 2 [file ffbonded.itp, line 1250]:
Overriding Bond parameters.
old: 0.1522 167360 0.1522 167360
new: C CT 1 0.15 209200.0
WARNING 3 [file ffbonded.itp, line 1251]:
Overriding Bond parameters.
old: 0.123 518816 0.123 518816
new: C O 1 0.1215 585760.0
......
Generated 103714 of the 103740 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 70322 of the 103740 1-4 parameter combinations
ERROR 1 [file 5C8B.B99990002.top, line 11399]:
No default Bond types
....
ERROR 7 [file 5C8B.B99990002.top, line 42283]:
No default U-B types
....
ERROR 20 [file 5C8B.B99990002.top, line 59103]:
No default Ryckaert-Bell. types
....
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 2 [file 5C8B.B99990002.top, line 73884]:
System has non-zero total charge: -23.999995
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Removing all charge groups because cutoff-scheme=Verlet
There were 2 notes
There were 7 warnings
-------------------------------------------------------
Program grompp, VERSION 5.0.7
Source code file: /gromacs-5.0.7/src/gromacs/gmxpreprocess/grompp.c, line: 1728
Fatal error:
There were 50 errors in input file(s)
It seems, you have multiple errors in your topology file. This maybe associated with the coordinate (pdb or gro) file. Try to generate your topology taking pdb file from other sources.
Dear Jamoliddin Razzokov,
Many more thanks for your kind reply and regarding your suggestion can you elaborate bit more about perform this "Try to generate your topology taking pdb file from other sources" ?. It would be really helpful if you give me some guidance or source to read.
Thanking you in advance
Dear Jamoliddin,
I have used "https://cgenff.paramchem.org/" to generate topology. It works well so no need of suggestions.
Thank you
Well, it is just a warning. You can skip them at all if You set -maxwarn to some higher value than the number of Your warnings. Or it would be better to eliminate occurence of similar parameters in Your included topology file and inhome charmm36 force field bonded and non-bonded.itp... Maybe You put Your parameters in other section of topology file.
Dear All,
Many more thanks for your kind suggestions and finally I solved the issue using following steps
Step1: I Inspected the each problematic lines in topology file and took the respective 5 pairs of bonds and 2 angles as below:
x.top file:
3018 3019 1
3021 3022 1
3028 3029 1
3032 3033 1
3036 3037 1
3021 3023 3024 5
3021 3023 3025 5
Step2: Drew the atom types for each pair of bond and angles topologies
3018 3019 1 "CG31 H91"
3021 3022 1 "CG31 H91"
3028 3029 1 " CG31 H91"
3032 3033 1 " CG31 H91"
3036 3037 1 "CG31 H91"
3021 3023 3024 5 "CG31 CG32 H92 "
3021 3023 3025 5 "CG31 CG32 H92 "
Step3: Cross checked the above combinations of bond and angles in ffbonded.itp file but it was not there. Then I redefined these 7 missing parameters which solved my problem.
To conclude, grompp try to look for the above 7 problematic bond and angles in ffbonded.itp file but failed to find it out and end up giving all missing parameters as an error like no default bond, U-B types (angles).
Cheers
Also I would like to add one more point that be aware of comment syntax (its ";" for gromacs not "!" as like in cgenff format). I got some errors because of this very simple reason so be aware of it and make sure about the same.
Cheers
It seems you have not properly generated topology for your system.
You could do that using the following link:
http://www.swissparam.ch/
Follow the instructions, its very simple and efficient to use.
Hope it helps, all the best.
gromacs files are case sensitive - it might be, that the reason of Your novel problems is Your previous fault, which You showed in the begining of the post. You can simly put to lower case all names of atom types (not atom names) in the file, which You want to import in gromacs (which You generated with cgenff), and of course it will affect all other lines (angles, dihedrals, impropers) - it will eliminate the 'overriding problem' and, maybe, this one too. what does it mean - modified topology covalently bound to asp? bound with amide peptide bond or somehow else??
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