RE: Gromacs to Charmm FF Format Conversion -Reg

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Feb 12 2019 - 10:34:53 CST

Any particular reason you can't just use the native GROMACS inputs? http://www.ks.uiuc.edu/Research/namd/2.13/ug/node14.html The only thing you'll need to do is copy the #include'd files into the grotopfile, since NAMD won't follow include statments.

-Josh

On 2019-02-12 08:47:38-07:00 owner-namd-l_at_ks.uiuc.edu wrote:

---------- Forwarded message ---------
From: Mani Kandan <manikandand5110_at_gmail.com<mailto:manikandand5110_at_gmail.com>>
Date: Tue, Feb 12, 2019, 9:13 PM
Subject: Re: namd-l: Gromacs to Charmm FF Format Conversion -Reg
To: Lennart Nilsson <Lennart.Nilsson_at_ki.se<mailto:Lennart.Nilsson_at_ki.se>>

Yes, but I want the martini coarse grained force field v2.2. That was available in the gromacs format, I need an tool to convert into charmm format to use in namd.

On Tue, Feb 12, 2019, 9:10 PM Lennart Nilsson <Lennart.Nilsson_at_ki.se<mailto:Lennart.Nilsson_at_ki.se>> wrote:
Since GROMACS does not have a force field of its own, I believe that all force fields in GROMACS do exist in their own native formats (AMBER; CHARMM; OPLS; ..) and these can often be read directly by other programs (e.g, NAMD reads CHARMM FF files directly).

Best wishes,
Lennart Nilsson

From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] On Behalf Of Roessler, Bryan C
Sent: den 12 februari 2019 16:23
To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>; Mani Kandan <manikandand5110_at_gmail.com<mailto:manikandand5110_at_gmail.com>>
Subject: Re: namd-l: Gromacs to Charmm FF Format Conversion -Reg

You can play with the ParmEd program, but I have no personal experience using it: https://github.com/ParmEd/ParmEd

If you are trying to convert a standard FF, the CHARMM FF's are also available in the GROMACS format here: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

________________________________
From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> <owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>> on behalf of Mani Kandan <manikandand5110_at_gmail.com<mailto:manikandand5110_at_gmail.com>>
Sent: Tuesday, February 12, 2019 8:12:40 AM
To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>
Subject: namd-l: Gromacs to Charmm FF Format Conversion -Reg

Hi all,

             Is any tool available to convert gromacs force field into charmm format force field? Kindly let me know if any tool is available.

Thanks

With Regards
MANIKANDAN D

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