Re:

From: Babban Mia (babbanmia_at_gmail.com)
Date: Tue Aug 16 2011 - 09:41:58 CDT

On Tue, Aug 16, 2011 at 8:05 PM, Jeffrey J. Potoff <
jpotoff_at_chem1.eng.wayne.edu> wrote:

> 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
>

> * I did not quite understand this part ,Sir*
>

> 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
> *
> *

*Why are we saving it twice?
Can you break up the code and explain a bit more ?*

> 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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