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

[Justin Lemkul]

On 12/7/17 3:23 AM, Simon Kit Sang Chu wrote:
> 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?

You're trying to use CHARMM atom types with the AMBER force field. You 
can't just copy and paste parts of different force fields together. 
AMBER doesn't know what those atom types are in the .tdb hence you get a 
fatal error for the atom type (tpA).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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