AMBER Archive (2007)

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

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue May 08 2007 - 01:28:14 CDT

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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