On 20/02/2012 4:56 PM, 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
grompp is trying to construct a topology, and so needs to be able to
find a a suitable entry in [ atomtypes ] of ffnonbonded.itp. Later it
will need to find other related parameters for the new atom types.
atomtypes.atp serves other purposes (e.g. pdb2gmx).
Mark
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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