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

[Nash, Anthony]

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
alternatives?

Many thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London