This solved my problem, although I am not totally sure to have perfectly
understood how the .tdb had to be edited. I added the following entry:
[ MME-NH ]
[ delete ]
H
Anyway, it solved the problem I had.
Many thanks for your help!
Antoine
On 09/05/2011 09:54 AM, Mark Abraham wrote:
On 5/09/2011 6:41 PM, Delmotte, Antoine wrote:
Dear Gromacs users,
I am once again requesting your help for the editing of the opls
force field .rtp and .hdb files.
I have inserted the parameters for a new residue, N-methyl methionine
(MME). In this molecule, the methyl group is attached to the nitrogen
atom from the peptide bond, which I think is the origin of my problem.
pdb2gmx works fine and generates the topology files without any
error. Unfortunately, when I looked at the .gro file generated in
PyMol (after conversion to pdb with g_editconf), I realized that 3
hydrogens have been added to the nitrogen atom, so I effectively get
R2-N-H4:
H1 \ / CH3
H2 - N - CA - (rest of the aminoa acid)...
H3 / \ H
instead of R2-N-H:
CH3 \
N - CA - (rest of the aminoa acid)...
H /
My guess is that Gromacs automatically adds those 3 hydrogens because
MME is a terminal residue, but I don't know how to prevent pdb2gmx
from doing so.
That uses the .tdb terminal database system. You will need a custom
entry to generate your two hydrogen atoms, and to use pdb2gmx -ter to
get a chance to select it.
Separately, if this residue is ever to be a non-terminal one, you'll
need to define one H atom bound to the N atom in the .rtp entry, so do
that now.
Mark
I have tried different modifications in the .rtp file, including
using different atom types, removing the peptide bond (the line N -C
) in the list of bonds, changing the hdb file, but nothing seems to
have had any effect.
I guess I could also simply remove these hydrogens from the .gro and
.itp files after using pdb2gmx, but I would have a better confidence
in what I changed in the force field files if pdb2gmx was giving me
the right answer directly.
See below my .rtp and .hdb entries:
[ MME ]
[ atoms ]
N opls_238 -0.500 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_210 0.048 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
SD opls_202 -0.335 4
CE opls_209 -0.013 5
HE1 opls_140 0.060 5
HE2 opls_140 0.060 5
HE3 opls_140 0.060 5
C opls_235 0.500 6
O opls_236 -0.500 6
CM opls_244 -0.110 7
HM1 opls_140 0.037 7
HM2 opls_140 0.037 7
HM3 opls_140 0.037 7
[ bonds ]
N CA
N CM
CM HM1
CM HM2
CM HM3
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG SD
SD CE
CE HE1
CE HE2
CE HE3
C O
MME 6
1 1 H N CM CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG SD CB
3 4 HE CE SD CG
3 4 HM CM N CA
Once again, any idea about this problem would be greatly appreciated.
Thanks to all in advance.
Regards,
Antoine
On 08/26/2011 05:42 PM, Delmotte, Antoine wrote:
Oh, thank you so much! That was indeed the error.
It's amazing how these little things can sometimes drive you mad....
Thanks a lot,
Antoine
On 08/26/2011 05:27 PM, Thomas Piggot wrote:
Hi,
I think the problem is that you have a dash rather than a minus
symbol for the sign of the charge on the OD atom.
Cheers
Tom
Delmotte, Antoine wrote:
Dear Gromacs users,
I am currently trying to run an MD simulation with the OPLS-AA
force field on a protein having different non standard residues
and a ligand. I found the charges for the OPLS force field for
these residues in the literature and I am now trying to add them
in the OPLS force field parameter files.
I have edited the aminoacids.rtp and the aminoacids.hdb files for
the OPLS-AA force field, as well as the residuetypes.dat file.
Here is an example for one of the amino acids, hydroxyproline:
[ HYP ]
[ atoms ]
N opls_239 -0.140 1
CA opls_246 0.010 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_137 -0.120 3
HG1 opls_140 0.060 3
OD opls_167 −0.683 3
HD opls_168 0.743 3
CD opls_245 -0.050 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG OD
OD HD
CG CD
CD HD1
CD HD2
CD N
C O
-C N
[ impropers ]
-C CA N CD improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
When I run pdb2gmx, I get the following error, which is not very
informative:
All occupancies are one
Opening force field file
/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file
/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 58
-------------------------------------------------------
Program g_pdb2gmx, VERSION 4.5.3
Source code file:
/builddir/build/BUILD/gromacs-4.5.3/src/kernel/resall.c, line: 389
Fatal error:
in .rtp file in residue HYP at line:
OD opls_167 −0.683 3
I would be grateful if anyone could shed some light on the origin
of this error, and on what I can do to correct it.
I am using Gromacs 4.5.3.
Thanks a lot in advance,
Antoine
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