[gmx-users] modifying aminoacids.n.tdb in amber14sb.ff

[Simon Kit Sang Chu]

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