Re: dimer minimisation and psfgen problem

From: Uday Chippada (chippada_at_eden.rutgers.edu)
Date: Thu Mar 18 2004 - 14:44:35 CST

Hi guys,
I have asked this same question before with no luck.
How do I apply forces on 3 atoms simultaneously, for eg. if i have 3
chains, and I want to pull all three chains at same time, how do i
specify the SMD atom?
I mean to ask is there a way I can figure out which SMD atom is which,
from thep output log file.
Thanx
Uday.

> "I maybe wrong but I don't think namd will take more than one psf
file."
>
> No, you are not wrong :). Namd will even blurt out an error message
specifying that you try to load two structure files.
>
> "In any case you can (and should) combine this file using psfgen.
Just
> make sure to assign the chains different segment IDs and things will
be
> fine..."
>
> That's what I want to have help about. I want to run a minimisation
on a dimer but I am unsure about how to achieve this...
>
> here is the script I use with psfgen
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> topology top_all22_prot.inp
>
> segment IL8A {
> first NONE
> last NONE
> pdb IL8A.pdb
> }
>
> patch DISU IL8A:7 IL8A:34
> patch DISU IL8A:9 IL8A:50
>
> coordpdb IL8A.pdb IL8A
>
> writepsf output/IL8A.psf
>
> segment IL8B {
> first NONE
> last NONE
> pdb IL8B.pdb
> }
>
> patch DISU IL8B:7 IL8B:34
> patch DISU IL8B:9 IL8B:50
>
> coordpdb IL8B.pdb IL8B
>
> writepsf output/IL8B.psf
>
> guesscoord
> writepdb output/IL8dimr_out.pdb
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> What do I have to write in order to obtain a single psf with the two
segment?
>
> Thanks.
>

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