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

[Mark Abraham]

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
>>>>
>>>
>>
>>
>
>
>