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

Delmotte, Antoine antoine.delmotte09 at imperial.ac.uk
Mon Sep 5 12:56:26 CEST 2011


This solved my problem, although I am not totally sure to have perfectly 
understood how the .tdb had to be edited. I added the following entry:

[ MME-NH ]
[ delete ]
H

Anyway, it solved the problem I had.

Many thanks for your help!

Antoine

On 09/05/2011 09:54 AM, Mark Abraham wrote:
> 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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