[gmx-users] error in residue topology

[Chanchal]

Hi Justin,
  Thanks for the info. I know that the topologies are provided in that
website.  But they have used charmm27 ff and converted it to gromacs format.
But I want to use gromos96 45a3 ff.
I have another question. Suppose I use those topologies for dopc . And for
the sugar part, I use gromos96 45a3. Will it create problem when we combine
sugar /dopc system?
Thanks
Chanchal

On Tue, Aug 18, 2009 at 7:46 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Chanchal wrote:
>
>> Hi All,
>>   I am a novice in gromacs. I want to study sugar/membrane interaction and
>> I want to use gromos96 45a3 ff. At first  I am planning to simulate  dopc
>>  bilayer + water.  I downloaded the pdb file of dopc  from the site
>> http://www.bioinf.uni-sb.de/RB/ .  Then I typed pdb2gmx_d -f dopc.pdb and
>> choose gromos96 45a3 force field. But I got the error "Residue 'OLE' not
>> found in residue topology database". How can I fix the error?
>>
>
> This happens because pdb2gmx is not magic.  See here:
>
>
> http://oldwiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
>
> The website you reference provides suitable topologies for this type of
> simulation, making pdb2gmx unnecessary.
>
> -Justin
>
>  Thanks
>> Chanchal
>>
>>
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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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