[gmx-users] Amber 14SB force-field problem with residue HID

Kevin mcfc1301 at gmail.com
Fri Sep 13 01:08:57 CEST 2019

Dear Users,

I have encountered a problem with the Amber force-field downloaded from
http://www.gromacs.org/Downloads/User_contributions/Force_fields. Whenever
I feed this forcefield to pdb2gmx and get a residue HID for protein
topology, it will cause error message: "No default Proper Dih. types". This
error can simply be solved by swapping the second and third indices on the
line number given with the error message.

I tried to dig into the reason behind this error. First, the error line
contains atomtypes in a sequence of "CT  CC  CV  NA" which CANNOT be found
in ffbonded.itp. Instead, "CT  CV  CC  NA" can be found in ffbonded.itp and
I guess that is why my solution worked. However, when I look at the
topology of HID, I was confused:

[ impropers ]
    -C    CA     N     H
    CA    +N     C     O
    CG   CE1   ND1   HD1
    CG   NE2   CD2   HD2
   ND1   NE2   CE1   HE1
   ND1   CD2    CG    CB

Converting from atom name to atomtypes, there is no either "CT  CC  CV  NA"
or "CT  CV  CC  NA" in impropers. However, "ND1   CD2    CG    CB" is very
likely to be the folk just written in a reversed sequence. More
interestingly, I gave a try on the Amber ff99*-ILDN forcefield, the HID
topology appears to be nearly the same but no error message was produced.
The error was always found in the second [dihedrals] block, so I assume it
is referred to impropers. That gave me two questions:
1. How does impropers be constructed by pdb2gmx?
2. Why different forcefields seem to give different sequence of atomtypes
for imporpers.

In fact, Q2 makes absolutely no sense, so I think I must be missing

Any comment is greatly appreciated.

The Ohio State University

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