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

[Mark Abraham]

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
>>>
>>
>
>