VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 07 2009 - 09:39:42 CDT

On Wed, Oct 7, 2009 at 3:21 AM, Baofu Qiao <qiaobf_at_gmail.com> wrote:
> Hi Young-Min,
>
> Have you found some way to show the bonds in coarse grained model? Now I
> meet the same problem.

have you tried the top2psf script as i suggested in reply to the original mail?
n.b.: you have to use a top file that is generated _while_ generating your .tpr
file by giving the -pp option to grompp.

axel.

> best regards,
> Baofu Qiao
>
> BAN,YOUNG MIN wrote:
>> Hello.
>>
>> I am trying to represent DPPC lipids as bonds or lines. But since I am
>> using Marrink's coarse grained model, it seems that vmd does not
>> recognize bonding between coarse grained molecules. I am using
>> Gromacs, so I have .gro, .itp, and .top files.
>>
>> How can the lipids be represented by bonds or lines using those .gro,
>> .itp, or .top files? Do I need other type of files to do this?
>>
>> Thanks in advance.
>>
>> Young-Min Ban
>>
>>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.