[gmx-users] PSF file in martini force field

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jan 23 22:51:21 CET 2012

On 24/01/2012 8:39 AM, Li, Hualin wrote:
> Hi,Mark,
>       Thank you very much for your answer.  In this case , if I want to know about the protein structure(like bonding, angles...), Is there any method I can use please?

g_bond and g_angle allow you to measure bond lengths and angles of atoms 
in well chosen index groups.

>   The difficult part in this question may be that I have more than one proteins in the same output file(GRO),  I know some tcl script may draw the protein structure in CG  model (including bonding and secondary structures) one protein by one protein, but is there any method to draw the structure for all the proteins at the same time?

With suitable modification to their heuristics for guessing where bonds 
occur, various visualization packages can be useful. The GROMACS webpage 
has some suggestions.


>      Thanks again.
> --Hualin
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham [Mark.Abraham at anu.edu.au]
> Sent: Monday, January 23, 2012 3:22 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] PSF file in martini force field
> On 24/01/2012 4:20 AM, Li, Hualin wrote:
>> Hi all,
>>       I am running Gromacs on the system of several proteins on the membrane using martini force field.From the output files, if I want to generate the PSF files from them , is there any easy way to do it please?
> No GROMACS utilities will write a PSF for CHARMM input. Consult the
> CHARMM documentation.
> Mark
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> 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

More information about the gromacs.org_gmx-users mailing list