Hi everyone,
I am trying to add new terminal capping as VAL-NH2 in
amber14sb.ff/aminoacids.n.tdb. I refer to charmm36-nov2016 and created my
VAL-NH2 without caring about the charges first. Meanwhile, aminoacid.rtp
remains the same.
*aminoacids.n.tdb*
; manually added VALN ( VAL neutral - NH2 capping )
; reference : charmm36-nov2016.ff/merged.n.tdb GLY-NH2
[ VAL-NH2 ]
[ replace ]
N NH2 14.007 -0.96
CA CT2 12.011 0.10
HA HB2 1.008 0.09
[ add ]
1 4 H N CA C
H 1.008 0.34 -1
;[ delete ]
; H
*aminoacids.rtp*
[ VAL ]
[ atoms ]
N N -0.41570 1
H H 0.27190 2
CA CX -0.08750 3
HA H1 0.09690 4
CB 3C 0.29850 5
HB HC -0.02970 6
CG1 CT -0.31920 7
HG11 HC 0.07910 8
HG12 HC 0.07910 9
HG13 HC 0.07910 10
CG2 CT -0.31920 11
HG21 HC 0.07910 12
HG22 HC 0.07910 13
HG23 HC 0.07910 14
C C 0.59730 15
O O -0.56790 16
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 HG13
CG2 HG21
CG2 HG22
CG2 HG23
C O
-C N
[ impropers ]
-C CA N H
CA +N C O
gromacs returns a fatal error when I do pdb2gmx.
*pdb2gmx error*
Fatal error:
tpA = 53191, i= 0 in print_atoms
I tried to refer to another thread -
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-April/104774.html.
No solution was given at that time.
May anyone point out something I missed?
Regards,
Simon
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