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#36087 - 12/18/16 12:23 PM Force field transformation from Gromacs to Charmm
Dawid Offline
Forum Member

Registered: 12/05/16
Posts: 12
Dear All,

Have you ever seen a script/tool that allows for transformation of the Gromacs force field files
into CHARMM force field files? I can see that there is a Pythons script that does the other
way around.

Also I could use a tool that creates *.psf file from *.top file. I googled for that and found this

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/top2psf.pl

Would you recommend anything else?

Best regards,
Dawid Grabarek

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#36088 - 12/18/16 04:11 PM Re: Force field transformation from Gromacs to Charmm [Re: Dawid]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
This seems a bit backward - Gromacs does not have a forcefield, it just can use some publicly available forcefields. CHARMM can of course handle its own forcefield (Gromacs has a translation of part of the extensive CHARMM forcefield, but not all of it). Some of the many Amber force fields are also available in a CHARMM readable format.
You can create PSFs with CHARMM, either directly or via eg the CHARMM-GUI web interface; I would recommend starting with CHARMM since in this way you learn what is going on - there are examples in the Script Archive forum.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#36108 - 12/30/16 01:18 PM Re: Force field transformation from Gromacs to Charmm [Re: lennart]
Dawid Offline
Forum Member

Registered: 12/05/16
Posts: 12
Originally Posted By: lennart

You can create PSFs with CHARMM, either directly or via eg the CHARMM-GUI web interface; I would recommend starting with CHARMM since in this way you learn what is going on - there are examples in the Script Archive forum.



Yes, that's what I have decided to do after all.
I guess I have successfully created the PSF file but
I encountered something strange. Namely while the
number of bonds in CHARMM PSF and Gromacs TOP files is
the same for my protein, the number of angles and
dihedrals is by merely 1 lower in the former case.
Besides, number of CMAP and improper dihedrals is in
agreement according to both packages. I have
checked the protonation state of all residues and
terminating residues and they are exactly the same
when I use either of the packages.

Could you give me a clue on where this discrepancy may
come from, please? My PSF generation does not finish
with either warning or error.

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#36109 - 12/30/16 01:27 PM Re: Force field transformation from Gromacs to Charmm [Re: Dawid]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
If you use the CHARMM forcefield, CHARMM should generate a correct PSF; I have no idea why GROMAC is off. It may of course be that your setups are identical. CHARMM (normally) generates all possible angles and dihedral from the bonded topoogy.

I would assume that CHARMM is correct, but without knowning exactly what you are doing it is difficult to tell.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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