[gmx-users] Error in ligand coordinate file
Justin Lemkul
jalemkul at vt.edu
Wed Aug 8 17:10:09 CEST 2012
On 8/8/12 10:44 AM, sai nitin wrote:
> Hi justin,
>
> Ok i will explain more clearly what i really have is protein ligand
> complex from Autodock..I choose best complex based on predicted
> binding affinity. Using pymol i visualized complex.pdb and saved only
> ligand (ligand.pdb given below) and used swiss param tool online
> http://swissparam.ch/ to charmm 27 FF .itp file then i followed
> tutorial and ran 10ns simulation now wanted to use g_lie to calculate
> binding free energies..of this complex..so have to run one more
> simulation for ligand only in water right...for that im using
> coordinate file which i have saved it from pymol
> in original PDB file it is properly aligned :)
>
> ATOM 1 C <1> d 83.432 21.209 56.133 -0.07 -0.02 C
> ATOM 2 C <1> d 84.828 21.291 56.786 -0.29 0.00 C
> ATOM 3 O <1> d 83.629 21.200 54.697 -0.02 -0.07 O
> ATOM 4 C <1> d 85.679 20.564 55.751 -0.19 -0.02 C
> ATOM 5 C <1> d 85.046 21.032 54.436 -0.15 0.04 C
> ATOM 6 N <1> d 82.546 22.305 56.532 -0.10 -0.05 N
> ATOM 7 C <1> d 81.884 22.186 57.757 0.18 0.05 C
> ATOM 8 N <1> d 81.028 23.185 58.155 0.01 -0.07 N
> ATOM 9 O <1> d 82.069 21.213 58.493 -0.09 0.04 O
> ATOM 10 C <1> d 80.868 24.232 57.405 -0.07 0.06 C
> ATOM 11 C <1> d 81.567 24.413 56.119 -0.49 0.00 C
> ATOM 12 C <1> d 82.377 23.424 55.745 -0.38 0.02 C
> ATOM 13 N <1> d 80.012 25.195 57.842 0.39 0.02 N
> ATOM 14 H <1> d 79.062 24.997 58.139 -0.05 -0.06 H
> ATOM 15 H <1> d 80.312 26.164 57.884 -0.11 -0.01 H
> ATOM 16 O <1> d 84.944 20.703 58.090 0.01 0.19 O
> ATOM 17 H <1> d 85.311 19.798 57.956 -0.17 -0.58 H
> ATOM 18 O <1> d 85.512 19.135 55.900 0.09 0.57 O
> ATOM 19 H <1> d 84.884 19.014 56.648 -0.30 -0.75 H
> ATOM 20 C <1> d 85.627 22.354 53.918 -0.22 0.11 C
> ATOM 21 O <1> d 84.597 23.194 53.394 -0.56 -0.44 O
> ATOM 22 H <1> d 83.757 22.697 53.521 0.27 0.18 H
> END
>
> Im running PDB2GMX to generate topol.top file..for this ligand by
> CHARMM 27 FF but it gives following error
>
> Fatal error:
> Residue '<1>' not found in residue topology database
>
> So now question how to solve this error..? Can you please suggest some help ?
>
You say you used SwissParam, which should have given you a topology, correct?
If nothing else, it should have given you suitable parameters in some form,
after which you should follow what is described here:
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
pdb2gmx isn't magic. You need to tell it what all the ingredients are before
you expect it to produce a topology.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list