AMBER Archive (2009)

Subject: [AMBER] minimization to reduce covalent deviation

From: Peter Varnai (p.varnai_at_sussex.ac.uk)
Date: Mon Jun 01 2009 - 15:25:07 CDT

Hello,

I need to minimize a DNA structure so that the covalent deviations
become minimial from the respective force field value. The reason for
doing this after an explicit water dynamics is to limit the long list
of covalent violations that is calculated by the ADIT deposition
server of PDB. Such violations will enter the PDB header...

I tried conjugate gradient minimisation in explicit water environment
using sander in amber10 (no shake but the same pbc used in md) and
also tried stripping the water and using GB to reduce the degree
freedom. I can get the rms of the gradient below 0.01 kcal/mol/A after
a couple of thousand steps but not much lower. I would have thought
that this should be enough to be within say 0.015 A and 2 degrees from
the ff values (which are somewhat different from dictionary standard
used for nucleic acids by PDB). However, I get a long list of covalent
violations mostly for angles (about 4 degrees) and base planarity. Eg,
N3-C2-O2 in CYT is 116.2, equilibrium value in parm99.dat is 122.5 and
the standard value in PDB is 121.9.

I hoped that xmin will do a good job with GB but I already reported
that it ignores the drms exit criterion. I could try nmode's Newton
Raphson but it seems to be an overkill. Here I talk about minimization
without nmropt restraints that I will need to add back once I figured
out a good protocol. Any suggestions?

Regards,
Peter

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