[gmx-users] Error from residues added to rtp file
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Sep 5 10:54:01 CEST 2011
On 5/09/2011 6:41 PM, Delmotte, Antoine wrote:
> Dear Gromacs users,
>
> I am once again requesting your help for the editing of the opls force
> field .rtp and .hdb files.
>
> I have inserted the parameters for a new residue, N-methyl methionine
> (MME). In this molecule, the methyl group is attached to the nitrogen
> atom from the peptide bond, which I think is the origin of my problem.
>
> pdb2gmx works fine and generates the topology files without any error.
> Unfortunately, when I looked at the .gro file generated in PyMol
> (after conversion to pdb with g_editconf), I realized that 3 hydrogens
> have been added to the nitrogen atom, so I effectively get R2-N-H4:
>
> H1 \ / CH3
> H2 - N - CA - (rest of the aminoa acid)...
> H3 / \ H
>
> instead of R2-N-H:
>
> CH3 \
> N - CA - (rest of the aminoa acid)...
> H /
>
> My guess is that Gromacs automatically adds those 3 hydrogens because
> MME is a terminal residue, but I don't know how to prevent pdb2gmx
> from doing so.
That uses the .tdb terminal database system. You will need a custom
entry to generate your two hydrogen atoms, and to use pdb2gmx -ter to
get a chance to select it.
Separately, if this residue is ever to be a non-terminal one, you'll
need to define one H atom bound to the N atom in the .rtp entry, so do
that now.
Mark
>
> I have tried different modifications in the .rtp file, including using
> different atom types, removing the peptide bond (the line N -C ) in
> the list of bonds, changing the hdb file, but nothing seems to have
> had any effect.
>
> I guess I could also simply remove these hydrogens from the .gro and
> .itp files after using pdb2gmx, but I would have a better confidence
> in what I changed in the force field files if pdb2gmx was giving me
> the right answer directly.
>
> See below my .rtp and .hdb entries:
>
> [ MME ]
> [ atoms ]
> N opls_238 -0.500 1
> CA opls_224B 0.140 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_210 0.048 3
> HG1 opls_140 0.060 3
> HG2 opls_140 0.060 3
> SD opls_202 -0.335 4
> CE opls_209 -0.013 5
> HE1 opls_140 0.060 5
> HE2 opls_140 0.060 5
> HE3 opls_140 0.060 5
> C opls_235 0.500 6
> O opls_236 -0.500 6
> CM opls_244 -0.110 7
> HM1 opls_140 0.037 7
> HM2 opls_140 0.037 7
> HM3 opls_140 0.037 7
> [ bonds ]
> N CA
> N CM
> CM HM1
> CM HM2
> CM HM3
> CA HA
> CA CB
> CA C
> CB HB1
> CB HB2
> CB CG
> CG HG1
> CG HG2
> CG SD
> SD CE
> CE HE1
> CE HE2
> CE HE3
> C O
>
> MME 6
> 1 1 H N CM CA
> 1 5 HA CA N C CB
> 2 6 HB CB CG CA
> 2 6 HG CG SD CB
> 3 4 HE CE SD CG
> 3 4 HM CM N CA
>
> Once again, any idea about this problem would be greatly appreciated.
>
> Thanks to all in advance.
>
> Regards,
>
> Antoine
>
>
> On 08/26/2011 05:42 PM, 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....
>>
>> 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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