[gmx-users] Re: Only Ligand(Without Receptor) MD Simulation with solvent(other than water.)

[Justin Lemkul]

On 4/22/13 5:30 AM, Baptiste Demoulin wrote:
> Hi,
>
> You have to add an entry for the DRG residue in "aminoacids.rtp", in the
> gromos folder. Instructions on this can be found in the GROMACS manual
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>

This is not correct.  PRODRG produces a topology (albeit a very flawed one), so 
there is no need whatsoever to modify .rtp files since pdb2gmx should never be 
involved in this workflow.

-Justin

> 2013/4/22 zyduscadila <haresh.ajani at zyduscadila.com>
>
>> Dear Justin thanks for your email.
>>
>> I have tried those you mentioned in your email.
>>
>> I have submitted molecule of interest in PRODRG and got a DRG.itp or
>> DRG.pdb
>> file.
>>
>> I fired command pdb2gmx using DRG.pdb (obtained from PRODRG) using Gromos96
>> 43a1 force field , but I received the follwoing fatel error:
>>
>> "Residue "DRG" not found in residue topology database".
>>
>> Let me know, how to handle this error ? please give me a brief step how to
>> do this ?
>>
>> I hope you will give me a solution. Thanks in advance
>>
>> Thanks & Regards,
>>
>> HARESH AJANI
>>
>>
>>
>>
>> --
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>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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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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