[gmx-users] Error from residues added to rtp file

[Thomas Piggot]

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.