Problem to generate water segments and lipid reading in membrane

From: Leonardo Herrera (ldhz04_at_yahoo.com.mx)
Date: Tue Mar 10 2009 - 05:17:36 CDT

 
Hi, NAMD and VMD users
I write this post to find aid on the following problem.
I have a pair of severe problems to construct .psf. I have experience in NAMD with proteins, but my system at issue is a complex protein-membrane with 12500 water molecules.
My first question is how I cause that VMD writes the segment for my membrane (DMPC)? I have tried of many ways but more than I have obtained as exit is a lipid.
Second like I can generate loop of segments to construct atom segments (waters) with a maximum of 999 residues o molecules (2997 atoms) by chain and that these run of “A… Z”,
And third as I can realise second, starting off of I number of atom and of I do not number of remainder.
In the present message annex script to construct my membrane.psf
Thanks in advance.
Leonardo.
 
############
##Script job membrane
############
mol load pdb /Users/LEO/Desktop/Mem_H2O.pdb
mol load pdb /Users/LEO/Desktop/Mem_lipids.pdb
mol load pdb /Users/LEO/Desktop/Mem_ions.pdb
 
##psfgen
package require psfgen
 
##topology 
topology Users/LEO/Desktop/top_all27_prot_lipid_na.inp 
 
##Segment membrane
segment L {
first NONE
last  NONE
esids 1 DMPC
pdb /Users/LEO/Desktop/Memb.pdb
}
coord L 1 N {0.0 0.0 0.0}
coordpdb /Users/LEO/Desktop/Memb.pdb L
 
 
##Segment water
pdbalias residue HOH TIP3
set sel [atomselect top water]
set segnames [lsort -unique [$sel get segname]]
$sel delete
foreach segname $segnames {
set sel [atomselect top "segname $segname"]
$sel coordpdb /Users/LEO/Desktop/Memb.pdb
$sel delete
}
#segment W {auto none
#pdb /Users/LEO/Desktop/Mem_H2O.pdb
#}
#pdbalias atom HOH O OH2
#coordpdb /Users/LEO/Desktop/Mem_H2O.pdb W
 
##coor?
guesscoord
 
##write psf and pdb
writepdb /Users/LEO/Desktop/Mem.pdb
writepsf /Users/LEO/Desktop/Mem.psf

MenB Leonardo David Herrera Zúñiga

POSGRADO EN QUÍMICA  UAMI Biofisicoquímica
Universidad Autonoma Metropolitana IztapalapaTel. +52 (55) 5804 4674    ldhz04_at_yahoo.com.mx

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:35 CST