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
--
Dr Thomas Piggot
University of Southampton, UK.
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