AMBER Archive (2009)

Subject: [AMBER] input coordinates for vdW transition step in Amber 10 TI

From: Jodi Hadden (jodih_at_uga.edu)
Date: Wed Jun 10 2009 - 15:27:16 CDT

Hello all,

I am trying to run TI in Amber 10 on a system where TYR is mutated to
PHE. I have set up my inputs according to Thomas Steinbrecher’s online
tutorial (A9 on the Amber Tutorials page.)

The first step of my calculation, where TYR partial charges are
removed, seems to run just fine. However, when I begin the second
step, where the vdW transition is performed and TYR is mutated into
PHE, I run into a problem.

Here is the group file for the minimization at the first point of
quadrature for the second step:
-O -i mut_min_v0_01.in -o mut_min_v0_01.o -p TYR_complex.prm -c
rem_md_v0_12.rst -ref rem_md_v0_12.rst -r mut_min_v0_01.rst
-O -i mut_min_v1_01.in -o mut_min_v1_01.o -p PHE_complex.prm -c
rem_md_v1_12.rst -ref rem_md_v1_12.rst -r mut_min_v1_01.rst

The error tells me that for my v1 process, my topology and coordinate
files don’t match in atom number. I understand this, since the
topology file is for PHE while the input coordinate file is from the
data collection MD of the last point of quadrature from step one,
where the partial charges of TYR were being removed, and therefore
refers to atoms for TYR, not PHE. What I do not understand is: if I
can’t use this for my input coordinate file for the v1 process, what
am I supposed to use?

rem_md_v1_12.rst does not match PHE_complex.prm in atom number, and
the PHE_complex.rst coordinate file built along with PHE_complex.prm
in leap does not match rem_md_v0_12.rst (which I will still use for
process v0, yes?) in coordinate positions. I can’t see any other
options.

I suppose I could take rem_md_v0_12.rst (or rem_md_v1_12.rst since
they are the same) convert it to a pdb, make the mutation TYR->PHE and
run it through leap to create a new .rst file that has coordinates
that match rem_md_v0_12.rst, but refers to atoms of PHE, and maybe
that would solve my problem. But since this step is not mentioned in
the tutorial or the Amber manual, it seems there is an easier solution
that I can’t figure out because I misunderstood the tutorial or have
missed something somewhere.

If anyone could help me see my mistake, I would greatly appreciate it.
- Jodi

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