[gmx-users] problem in dna-protein simulation

[Bhanu]

Edit your pdb as per ur rtp file / forcefield.

On 16/06/2009, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> nitu sharma wrote:
>
>> Dear all,
>>
>>                    i am trying to simulation of dna-protein complex using
>> gromacs with amber port . I am using amber99 port with gromacs-4.0.3
>> version. I am facing problem in running pdb2gmx command .The error comes
>> like this-
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 4.0.3
>> Source code file: resall.c, line: 426
>>
>> Fatal error:
>> Residue 'T' not found in residue topology database
>>
>> Can anyone suggest me how  can I overcome this problem .
>>
>>
>
> http://oldwiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
>
> -Justin
>
> Thanks a lot in advance.
>>
>> Nitu sharma
>> Jawaherlal Nehru University
>>
>>
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>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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