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

Nash, Anthony a.nash at ucl.ac.uk
Tue Feb 23 11:02:59 CET 2016

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. 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), 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). But mean while
using Avogadro to build test structures is taking forever! Any

Many thanks

Dr Anthony Nash
Department of Chemistry
University College London

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