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

[Baptiste Demoulin]

Sorry, I didn't know about PRODRG. The use of it may be incorrect here,
since the error highlighted concerns pdb2gmx.


2013/4/22 Justin Lemkul <jalemkul at vt.edu>

>
>
> 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<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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>>> Receptor-MD-Simulation-with-**solvent-other-than-water-**
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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