[gmx-users] parametrization of GABA for charmm27

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Mon Dec 15 23:09:07 CET 2014


I have parametrized gamma-aminobutyric acid (GABA; three-letter residue
code ABU) for charmm27, which lacked it. This is essentially a hybrid of
glutamate and lysine parameters. I thought this would be a reasonable
starting point especially seeing as there is an overlap point at Glu CB
and Lys CD, which share a charge of -0.18

I would like to add my changes to the topologies archive
for the benefit of other users but the "attach file" link is greyed out.
Instead I copy them into this email.

There are, however, some problems where pdb2gmx changes things (at least
version 4.6.1 which I am using):
1. The charges of the carboxyl group are changed such that the topology
doesn't end up with 0 charge. This needs to be manually corrected at
2. It also adds 3 extra hydrogens to the amino group (a total of 6 rather
than 3), which also have to be removed manually from the topology and
output structure. This requires additionally that the atoms be renumbered
to continue consecutively.
3. As GABA lacks a carboxyl group on the amino carbon (CA) it has two
hydrogens, which are correctly added. However the topology says that it is
CT1 rather than CT2. This needs to manually corrected too, especially
seeing as no N-CT1-H Urey-Bradley parameters exist.

Here are the lines I added into aminoacids.rtp

[ ABU ]
 [ atoms ]
        N       NH3     -0.30   0
        H1      HC      0.33    1
        H2      HC      0.33    2
        H3      HC      0.33    3
        CA      CT2     0.21    4
        HA1     HA      0.05    5
        HA2     HA      0.05    6
        CB      CT2     -0.18   7
        HB1     HA      0.09    8
        HB2     HA      0.09    9
        CG      CT2     -0.28   10
        HG1     HA      0.09    11
        HG2     HA      0.09    12
        C       CC      0.62    13
        OT1     OC      -0.76   14
        OT2     OC      -0.76   15
 [ bonds ]
        CB      CA
        CG      CB
        C       CG
        OT2     C
        N       H1
        N       H2
        N       H3
        N       CA
        CA      HA1
        CA      HA2
        CB      HB1
        CB      HB2
        CG      HG1
        CG      HG2
        C       OT1
 [ impropers ]
        C       CG      OT2     OT1

and here are the lines I added into aminoacids.hdb

ABU     4
3       4       H       N       CA      CB
2       6       HA      CA      N       CB
2       6       HB      CB      CA      CG
2       6       HG      CG      CB      C

Perhaps someone can see from these lines what is causing the strange
problems above..

Best wishes

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