[gmx-users] Amber 14SB force-field problem with residue HID
jalemkul at vt.edu
Sun Sep 15 12:47:46 CEST 2019
On 9/12/19 7:08 PM, Kevin wrote:
> 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.
I don't generally use AMBER force fields so I can't comment on the issue
specifically, but be advised that nothing in the User Contribution
section of the website is validated in any way. We have asked users to
provide such testing (e.g. energies in AMBER vs. GROMACS) and there is
generally little or no follow-through, which is why those force fields
do not become officially included.
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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