[gmx-users] Using CHARMM force fields in Gromacs, pt. 2

[Peter C. Lai]

Make a copy of the original Charm36.ff (to say, charmm36cgen.ff) then patch 
your cgenff conversion into it.

To keep things sane, I contained my cgenff conversion into its own
ffbondedcgen.itp/ffnonbondedcgen.itp and included those .itps into the
charmm36cgen.ff/forcefield.itp
I also created separate cgen.rtp and cgen.hdb files and put them into
charmm36cgen.ff as well.

You've already figured out how to patch forcefields.dat so that's fine.

On 2012-02-20 01:56:04PM +0800, Jernej Zidar wrote:
> Hi.
>    Several months ago I was asking how to import and use two CHARMM
> forcefields in Gromacs at the same time in MD simulations. The two
> forcefields are CGENFF and CHARMM36.
> 
>   I was able to add the polymer monomers and relevant parameters so I
> can now create a pair of top/gro files directly using the pdb2gmx
> utility. I have also added some lipid molecules to the Gromacs version
> of CHARMM36.
> 
>    I was able to solvate the CGENFF-generated compound using the command:
> genbox -cp poly-1-1-1-1-1-new.gro -cs spc216.gro -p poly-1-1-1-1-1.top
> -o wpoly-1-1-1-1-1.gro
> 
>   But I can't neutralize the system using the following command:
> grompp -f em.mdp -c wpoly-1-1-1-1-1.gro -p wpoly-1-1-1-1-1.top -o ions.tpr
> 
>   To solve the problem I First tried including the spc.itp file from
> CHARMM36 but that didn't work because of the missing atomtypes in
> CGENFF's atomtypes.dat file. Oddly, adding the two missing atomtypes
> to ./cgenff/atomtypes.dat didn't help:
> Program grompp, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/toppush.c, line: 1166
> 
> Fatal error:
> Atomtype OW not found
> 
>   Then I tried to include the forcefield.itp from CHARMM36 + CHARMM36
> parameters for SPC water. Again it didn't help:
> ERROR 1 [file forcefield.itp, line 1]:
>   Incorrect number of atomtypes for dihedral (0 instead of 2 or 4)
> 
> ERROR 2 [file forcefield.itp, line 2]:
>   Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
> 
> ERROR 3 [file forcefield.itp, line 3]:
>   Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
> 
> ERROR 4 [file forcefield.itp, line 4]:
>   Incorrect number of atomtypes for dihedral (3 instead of 2 or 4)
> 
> ERROR 5 [file forcefield.itp, line 5]:
>   Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
> 
> ERROR 6 [file forcefield.itp, line 6]:
>   Incorrect number of atomtypes for dihedral (0 instead of 2 or 4)
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/topio.c, line: 668
> 
> Fatal error:
> Syntax error - File forcefield.itp, line 13
> Last line read:
> ' 1	2	yes	1.0	1.0'
> Found a second defaults directive.
> 
>   I get NO errors if I do a minimization of my compund in vacuo only
> using CGENFF.
> 
>   Could someone please advice what is the best course of action if one
> wants to use CHARMM36 and CGENFF together in one simulation?
> 
> Thanks in advance,
> Jernej Zidar
> -- 
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-- 
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Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
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