[AMBER] Batch Minimization

From: Abdul-Rashid III Sampaco <absampaco.up.edu.ph>
Date: Sun, 26 Nov 2017 11:24:56 +0800


I have a 1000ns netcdf trajectory file (i wrote a new structure every 1ps
so the file contains 1 million structures). It is basically a
conformational search of a small peptide. Is it possible to perform energy
minimization on all the structures in the file without having to rewrite
each one to a new file and iterating over them with a separate sander
command? Thanks.

I have already tried using the nc file as an input to sander like as

sander -O -i min.in -o min.out -c md.nc -r min_md.rst -p md.parm7

It turns out sander only accepts crd and rst7 files.

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Received on Sat Nov 25 2017 - 19:30:01 PST
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