On 27/08/2011 2:42 AM, 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....
I think the real lesson is to learn to edit documents that will contain
nothing but text using an editor that can be relied upon to produce only
plain text. Otherwise you spend your valuable time managing things that
computer programs should be managing for you.
Mark
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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