[gmx-users] pdb file of polymer

[Parvez khan]

thanx a lot Justin for reply

Regards
parvez

On Fri, Jun 29, 2012 at 2:27 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 6/29/12 2:21 PM, Parvez khan wrote:
>>
>> Hi, I am trying to do polymer simulation with gromacs. I am new to
>> gromacs and trying to construct topology for a system of polymer
>> chains. My problem is that i am facing difficulties to creat pdb file
>> for polymer chain containing 1000 monomers. I have used PRODRG server
>> but it gives me a pdb and topology file up to maximum 41 monomers
>> chain. I am not understanding what wrong with PRODRG server. Is there
>
>
> Nothing is wrong.  It's just that PRODRG limits how many atoms are allowed
> in the input structure.
>
>
>> any server or tool for generating db file.
>
>
> There are lots of ways to generate a coordinate file.  Here are some
> suggestions:
>
> http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
>
> -Justin
>
> --
> ========================================
>
> 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
>
> ========================================
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists