[gmx-users] generating an initial structure with a gromacs compatible tool

Mark Abraham mark.j.abraham at gmail.com
Wed Feb 24 15:05:01 CET 2016


On Tue, Feb 23, 2016 at 11:03 AM Nash, Anthony <a.nash at ucl.ac.uk> wrote:

> Hi all,
> Is there a friendly Gromacs compatible tool for generating a .gro/.pdb
> file using a specific forcefield topology specification within Gromacs
> itself? For context:
> I¹m in the process of fully parameterising five custom protein residues
> for the amber forcefield from ab initio calculations. Fragment #1 has been
> very successfully, with a production NPT simulation showing very little
> deviation from the equilibrium ab initio structure.
> Fragment #2, on the other hand, is driving me crazy. I derive partial
> charges, force constants, then I take the equilibrium structure, and
> replace the capped backbone ends (required for RESP) with NGLY and CGLY. I
> am using Avogadro to do this, which spits out a awful .pdb file which
> requires a lot of rearranging to be compatible with the atom order of the
> residues inside aminoacid.rtp in the amber99sb.ff.

But the .rtp entry is based on atom names. Atom order isn't significant
until grompp (and then it merely warns if the atom order of the input .gro
file does not match that of the .top). And you have an .rtp entry already,
what are you getting from Avogadro anyway?

I hold the eq_structure
> fixed in avogadro and run an energy equilibrium over the new adjoining
> glycine residues. All appears fine, until I run a Gromacs energy
> minimisation. The entire customer residue expands gently (beyond the eq
> distances, by a few angstrom),

Clearly your energy minimization isn't using constraints. Should it? You
need to understand the basis under which Avogadro is parameterizing for
this force field...

> and then an NVT simulation throws out a lot
> of LINCS warnings.
> I am pretty confident that this is the fault of my initial structure, in
> particular the angles (I¹m going to double check the FCs).

The simplest explanation is that you are mangling the atom order so that
the topology mdrun understands isn't the one you intend. But that comes
down to what you have in your .rtp/.itp files.

> But mean while
> using Avogadro to build test structures is taking forever! Any
> alternatives?

acpype is popular conversion tool for AMBER topologies, I understand.


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