[gmx-users] Error in ligand coordinate file

[sai nitin]

Hi justin,

Yes swiss param gave me ligand.itp file which gromacs topologies i
included in topol.top file which i generated ..usign PDB2GMX so no
need of creating seperate topol.top file for ligand only? can i use
same topol.top file to run MD to simulate only ligand because current
topol.top file has topologies for both ligand and protein..

Please help

Nitin

On Wed, Aug 8, 2012 at 5:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
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-- 

Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060