AMBER Archive (2009)

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

Date: Thu Jun 11 2009 - 05:42:51 CDT

Hi Jodi,

as Tom already mentioned, the tutorial does not assume that you run your
second TI step starting from the coordinates of the last step of the
first. All transformation substeps and even all lambda-points can be run
independently from each other. I see no benefit from starting from a
structure that has been simulated longer with a different potential
funtion beforehand, you will have to equilibrate at each new lambda-point

What you wanted to do works of course, but you would have to build the
PHE-containing coordinate file somehow (probably the way you mentioned it,
by generating a pdb, changing it and rereading it into leap). Otherwise,
you could build, from whatever your initial structure is, new crd files
for both the TYR and the PHE case and equilibrate them both together with
icfe=1 (with no charges of course). The later approach is what I normally

I know the setup of TI calculations as it is can be counterintuitive
sometimes, but I see no good way of making it better for cases like the
one you mentioned.

Kind Regards,


On Wed, June 10, 2009 4:27 pm, 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
> 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 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
> _______________________________________________
> AMBER mailing list

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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