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
När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>.
Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:20:30 CST