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

[Delmotte, Antoine]

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
>>
>