AMBER Archive (2007)

Subject: Re: AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains.

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue May 08 2007 - 06:11:42 CDT

I'm not familiar with the restraint definition that you used, are you
following the manual
or one of the tutorials? I don't see any use of "iatms" in the manual. Check
page
178 in the Amber9 manual for correct variables.

 I also do not think Amber supports dihedral restraints using center
of mass, only distances between centers of mass.

Have you already used Amber to perform normal (non-PMF) simulations?
You'll want to make sure everything is set up properly before you start
trying
restraints.
good luck

On 5/8/07, Catein Catherine <askamber23_at_hotmail.com> wrote:
>
> Dear All,
>
> I am trying to calculate the PMF for a system, with the four domains:
> Domain 1 to domain 4.
>
> Domain1---Domain2
> |
> Domain4---Domain3
>
>
> I tried to define the in file as follows (with the center of mass defined
> for each domain):
>
> &wt type='DUMPFREQ', istep1=10 /
> &wt type='END' /
> DISANG=xxx.RST
> DUMPAVE=xxx_vs_t.10
>
> =====xxx.RST to study the Gibbs free energy vs different dihedral angle of
> different domains======
>
> # Dihedral restrainst
> &rst iatms(1)=1/33, iatms(2)=34/64, iatms(3)=65/94, iatms(4)=95/126,
> iatms(5)=127/177, iatms=1,2,3,4, r1=0., r2=90., r3=180., r4=360., rk2 =
> 30.,
> rk3= 30.0, /
>
> =====xxx.RST to study the Gibbs free energy vs different distance of
> domain
> 1 and 2========
>
> # Distance restrainst
> &rst iatms(1)=1/33, iatms(2)=34/64, iatms=1,2, r1=0., r2=2., r3=5.,
> r4=10.,
> rk2 = 30., rk3= 30.0, /
>
>
> =============================================================================
>
> It is the right way to define the RST and in files for the PMF
> calculations?
> Did I miss a lot of things here, as I cannot get the xxx_vs_t.10 files
> after submit the jobs?
>
> Best regards and many thanks!
> Cat.
>
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