[gmx-users] my modified residue falls apart after MD
refmac5 at gmail.com
Thu Nov 23 03:57:50 CET 2017
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
I got complaint from gromacs.. I modified the SG-OE bond from S-O bond and
it should work...
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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