[gmx-users] Error in ligand coordinate file

[Justin Lemkul]

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

-- 
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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

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