VMD-L Mailing List

From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Wed Jun 08 2005 - 12:55:21 CDT

Hello to everyone

I am new in NAMD, and I am trying to use CHARMM program to analyze my
NAMD dcd trayectories, as in the manual is said to be posible. I found
this thread in VMD site:
 
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3561.html

which talks about the dificulties of translating X-plor Psf files to
Charmm ones or vice-versa.
Most of analysis programs of CHARMM requires psf files to be in CHARMM
format (I have not found a comand to allow x-plor formated psfs). In
the thread above is said the psfgen command "writepsf" can write
x-plor and charmm psf files using
  
writepsf [xplor|charmm] file.psf

so I modify a vmd tcl script I wrote with lines stolen from various
other scripts, which use to solvate and ionize my protein:

##############################################
1 mol load pdb 1UBQ.pdb
2
3 set ubq [atomselect top protein]
4 $ubq writepdb ubq-p.pdb
5
6 package require psfgen
7 topology /home/RPMs/NAMD/toppar/top_all22_prot.inp
8 pdbalias residue HIS HSE
9 pdbalias atom ILE CD1 CD
10 segment PROT {pdb ubq-p.pdb}
11 coordpdb ubq-p.pdb PROT
12 guesscoord
13 writepdb ubq.pdb
15 writepsf charmm ubq.psf
16
17 package require solvate
18 solvate ubq.psf ubq.pdb -t 5 -o ubq-wb
19
20 mol load psf ubq-wb.psf
21 mol load pdb ubq-wb.pdb
22
23 set everyone [atomselect top all]
24 measure minmax $everyone
25 measure center $everyone
26
27 package require autoionize
28 autoionize -psf ubq-wb.psf -pdb ubq-wb.pdb -is 0.00 -o ubq-wb-ionized
29 exit
############################################

the script works well if the option "charmm" in line 15 is omited .
Nevertheless, if I use it, it crashes after line 18 with the following
message:

PSF file is in CHARMM format; XPLOR format required.
error reading atoms

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

I dont know, but maybe solvate cannot use charmm-format psfs. At least
I haven't found a way to make solvate work in that context. As
autoionize cannot be called, I dont now either whether it allows
charmm psfs. Taking this into account, I would like to ask two
questions:

1) It is posible to modify this script to obtain a charmm psf of my
protein solvated and ionized? I thought it may be posible using a
modified solvate and autoionize routine, but I dont know if someone
have done this before, or where ca i find them.

2) Are dcd files psf-format independent, so a dcd file created using a
x-plor psf can be read after modifiing the psf to charmm format? if
is posible, I would be able to analyze my x-plor psf-generated
trayectories in charmm, otherwise I'll have to do all again.

  any help or suggestion is greatly acknowledged

Leonardo