Re:

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Tue Aug 16 2011 - 09:35:20 CDT

Maybe this example will help. This is a TCL script to build a PSF for a
solvated lipid bilayer using the MARTINI force field. Notice the water
has been split into two segments. In the PDB, the segname field is
"WAT1" and "WAT2".

psfgen <<ENDMOL
topology top_martini.inp

segment POPA {
 auto angles
 pdb popc_b1.pdb
 first none
 last none
}
segment POPB {
 auto angles
 pdb popc_b2.pdb
 first none
 last none
}

segment WAT1 {
 auto none
 pdb water_b1.pdb
 first none
 last none
}

segment WAT2 {
 auto nonepsfgen <<ENDMOL
topology top_martini.inp

segment POPA {
 auto angles
 pdb popc_b1.pdb
 first none
 last none
}
segment POPB {
 auto angles
 pdb popc_b2.pdb
 first none
 last none
}

segment WAT1 {
 auto none
 pdb water_b1.pdb
 first none
 last none
}

segment WAT2 {
 auto none
 pdb water_b2.pdb
 first none
 last none
}

coordpdb popc_b1.pdb POPA
coordpdb popc_b2.pdb POPB
coordpdb water_b1.pdb WAT1
coordpdb water_b2.pdb WAT2

writepsf start-cg.psf
writepdb start-cg.pdb

 pdb water_b2.pdb
 first none
 last none
}

coordpdb popc_b1.pdb POPA
coordpdb popc_b2.pdb POPB
coordpdb water_b1.pdb WAT1
coordpdb water_b2.pdb WAT2

writepsf start-cg.psf
writepdb start-cg.pdb

Anna James wrote:
> I understood your point but I use the following script on my
> solvent.pdb generated using packmol to get the psf out of it.
>
> package require psfgen
> topology topology27.inp
>
> pdbalias residue HIS HSE
> pdbalias atom ILE CD1 CD
>
> segment QQQ {pdb solvent.pdb}
> coordpdb solvent.pdb QQQ
>
> guesscoord
> writepdb solvent.pdb
> writepsf solvent.psf
>
> How do I generate psf file that could accomodate multiple segments?
> .Please suggest me changes in the above script.
> I could do with two more segments giving me 9999*2 extra residues
> (naming TTT and RRR) and I could possibly make required changes in the
> solvation script to consider the two more SEGIds
>
> In anticipation of an encouraging reply
>
>
> Anna James Vaughan
> Leeds
>
> > Date: Tue, 16 Aug 2011 09:43:00 -0400
> > Subject: Re: namd-l:
> > From: akohlmey_at_gmail.com
> > To: annajamesmatrix_at_hotmail.com
> > CC: namd-l_at_ks.uiuc.edu
> >
> > On Tue, Aug 16, 2011 at 9:38 AM, Anna James
> <annajamesmatrix_at_hotmail.com> wrote:
> > > Hello NAMD Experts
> > >
> > >
> > > I have a query about setting up a PBC unit.Unfortunately I am
> working with a
> > > large Globular Protein,the extent of which is around 90A in all
> the three
> > > X,Y Z axes that would mean My PBC Unit has to be larger than it to
> encompass
> > > the whole protein. I Created a Methanol Box of 100*100*100 A and
> filled it
> > > up with Methanol molecules as the per the density of Methanol .The
> number of
> > > Molecules exceeded 35000 and VMD/PSFGEN cannot process PDBs that have
> > > residues more than 9999.
> >
> > just use multiple segments (and multiple files). the numbers
> > can start fresh for each segment.
> >
> > axel.
> >
> > >
> > > I am sure lot of people would have worked with PBC units as large
> as 90A
> > > ,What is the way to go about solvating them ?Do we have to
> compromise on the
> > > number of Methanol Molecules while setting up the system?
> > >
> > > I am using the following parameters :
> > >
> > > exclude scaled1-4
> > > 1-4scaling 1.0
> > > cutoff 12.0
> > > switching on
> > > switchdist 10.0
> > > pairlistdist 14.0
> > > timestep 2.0
> > > rigidBonds all
> > > nonbondedFreq 1 .
> > >
> > > Looking at the above parameters, What would be the safe distance
> between the
> > > images while setting up PBC units?
> > > Are the above parameters good enough ?
> > >
> > >
> > > In anticipation of an encouraging reply
> > >
> > >
> > > Anna James Vaughan
> > > Leeds
> > >
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com http://goo.gl/1wk0
> >
> > Institute for Computational Molecular Science
> > Temple University, Philadelphia PA, USA.
> >

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
======================================================================

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