[gmx-users] my modified residue falls apart after MD
jalemkul at vt.edu
Thu Nov 23 04:01:22 CET 2017
On 11/22/17 9:57 PM, MD wrote:
> Thanks Justin. Then do I need to create new bond of SG and OE in
> ffbonded.itp? Cause I have tried adding SG and OE bond in ffbonded.itp and
SG and OE are atom names, not types. That's not a valid approach.
> I got complaint from gromacs.. I modified the SG-OE bond from S-O bond and
> it should work...
The [bonds] section requires atom names in order to function, so use of
SG and OE here is correct (your original entry used S and O, which are
atom types and therefore not correct). If grompp subsequently complains
about missing force field parameters when the correct bonds are written
to the topology, then what you're attempting to do is not supported by
the force field and you will have to either parametrize those missing
interactions or find parameters.
> On Wed, Nov 22, 2017 at 9:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 11/22/17 9:32 PM, MD wrote:
>>> Hi gromacs folks,
>>> I was trying to introduce sulfenic acid as modified cysteine to the
>>> forcefield as following. Everything went well until the "gmx mdrun -v
>>> -deffnm em". The only file I modified was merged.rtp since there were no
>>> new bond or dihedral angles. However my sulfenic acid falls apart (oxygen
>>> and sulfur are far away from the protein) after mdrun. Any help or
>>> suggestions what I should do next? I am reading the manual at the same
>>> but I thought maybe I can get some help here as well.
>>> Thank you for your time and any advice will be appreciated.
>>> [ CSO ]
>>> [ atoms ]
>>> N NH1 -0.470 0
>>> HN H 0.310 1
>>> CA CT1 0.070 2
>>> HA HB1 0.090 3
>>> CB CT2 -0.110 4
>>> HB1 HA2 0.090 5
>>> HB2 HA2 0.090 6
>>> SG S 0.6 7
>>> OE O -0.83 8
>>> HE1 H 0.160 9
>>> C C 0.510 10
>>> O O -0.510 11
>>> [ bonds ]
>>> CB CA
>>> S CB
>>> S O
>>> N HN
>>> N CA
>>> C CA
>>> C +N
>>> CA HA
>>> CB HB1
>>> CB HB2
>>> OE HE1
>>> O C
>> You need a bond between SG and OE.
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> jalemkul at vt.edu | (540) 231-3129
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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