Yulian Gavrilov wrote:
Dear Justin, gmx users,
I forgot to write, but I added these new residues to aminoacids.rtp.
Maybe I need to add them also to aminoacids.r2b? How to do it correctly?
An .r2b entry is unnecessary in this case; these files are only used to
standardize force field-specific names for certain residues.
Just new lines in it or add them to lines of Gly and Lys? So, I suppose
it is all steps in
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
These should be all the necessary steps.
-Justin
[ LYQ ]
[ atoms ]
N N -0.41570 1
H H 0.27190 2
CA CT -0.07206 3
HA H1 0.09940 4
CB CT -0.04845 5
HB1 HC 0.03400 6
HB2 HC 0.03400 7
CG CT 0.06612 8
HG1 HC 0.01041 9
HG2 HC 0.01041 10
CD CT -0.03768 11
HD1 HC 0.01155 12
HD2 HC 0.01155 13
CE CT 0.32604 14
HE1 HP -0.03358 15
HE2 HP -0.03358 16
NZ N -0.64977 17
HZ1 H 0.38604 18
C C 0.59730 19
O O -0.56790 20
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
C O
-C N
[ impropers ]
-C CA N H
CA +N C O
[ GLQ ]
[ atoms ]
N N -0.41570 1
H H 0.27190 2
CA CT -0.02520 3
HA1 H1 0.06980 4
HA2 H1 0.06980 5
C C 0.59730 6
O O -0.56790 7
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA C
C O
-C N
[ impropers ]
-C CA N H
CA +N C O
--
Sincerely,
Yulian Gavrilov
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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