AMBER Archive (2009)

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

From: Ye MEI (
Date: Thu Jun 11 2009 - 03:22:34 CDT

Hi Jodi,
TI with different number of atoms is only allowed when soft-core
potential is implemented. Those "scmask"ed atoms can be different in
two prmtop files, and other atoms should have their coordinates
In the first step of your simulation, only TYR is considered. In the 2nd
step, two prmtop files with different number of atoms are considered,
but you have only one coordinates file from the 1st step. So you need to
do some modifications by adding or removing atoms from the coordinates
file. You can write a simple code to do this job. Be careful with the
format of coordinates file.
Good luck.


On 6/10/2009, "Jodi Hadden" <> wrote:

>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 Steinbrecherís 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 -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 -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 donít 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
>canít 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 canít see any other
>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 canít 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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