[gmx-users] Re: Only Ligand(Without Receptor) MD Simulation with solvent(other than water.)
jalemkul at vt.edu
Mon Apr 22 12:02:43 CEST 2013
On 4/22/13 5:30 AM, Baptiste Demoulin wrote:
> 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
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.
> 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
>> 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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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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