From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Mon May 30 2005 - 18:37:05 CDT
Hello
I want to run NAMD and analyze the .dcd using CHARMM. To create the
protein in a waterbox I use the following script in vmd using "vmd
-dispdev text -e script.tcl"
##############################################
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, any dynamics done with that files cannot be readed with
CHARMM, because X-PLOR is the default format for PSF files. If
"charmm" is used in line 15, the following error occurs:
vmd > mol load pdb 1UBQ.pdb
Info) Using plugin pdb for structure file 1UBQ.pdb
Info) Using plugin pdb for coordinates from file 1UBQ.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file 1UBQ.pdb.
Info) Analyzing structure ...
Info) Atoms: 660
Info) Residues: 134
Info) Waters: 58
Info) Segments: 1
Info) Fragments: 59 Protein: 1 Nucleic: 0
0
vmd > set ubq [atomselect top protein]
atomselect0
vmd > $ubq writepdb ubq-p.pdb
Info) Opened coordinate file ubq-p.pdb for writing.
Info) Finished with coordinate file ubq-p.pdb.
vmd > package require psfgen
1.3.4
vmd > topology /home/RPMs/NAMD/toppar/top_all22_prot.inp
reading topology file /home/RPMs/NAMD/toppar/top_all22_prot.inp
>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> December 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
All comments to ADM jr. via the CHARMM web site: www.charmm.org
parameter set discussion forum
Created by CHARMM version 22 1
vmd > pdbalias residue HIS HSE
aliasing residue HIS to HSE
vmd > pdbalias atom ILE CD1 CD
aliasing residue ILE atom CD1 to CD
vmd > segment PROT {pdb ubq-p.pdb}
building segment PROT
reading residues from pdb file ubq-p.pdb
extracted 76 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.
vmd > coordpdb ubq-p.pdb PROT
reading coordinates from pdb file ubq-p.pdb for segment PROT
Warning: failed to set coordinate for atom O GLY:76 PROT
Warning: failed to set coordinate for atom OXT GLY:76 PROT
vmd > guesscoord
Info: guessing coordinates for 631 atoms (2 non-hydrogen)
Warning: poorly guessed coordinates for 5 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 MET:1 PROT
Warning: poorly guessed coordinate for atom HT2 MET:1 PROT
Warning: poorly guessed coordinate for atom HT3 MET:1 PROT
Warning: poorly guessed coordinate for atom OT1 GLY:76 PROT
Warning: poorly guessed coordinate for atom OT2 GLY:76 PROT
vmd > writepdb ubq.pdb
Info: writing pdb file ubq.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
vmd > writepsf charmm ubq.psf
Info: writing psf file ubq.psf
total of 1231 atoms
total of 1237 bonds
total of 2257 angles
total of 3293 dihedrals
total of 204 impropers
Info: psf file complete.
vmd > package require solvate
1.2
vmd > solvate ubq.psf ubq.pdb -t 5 -o ubq-wb
Info) Using plugin psf for structure file ubq.psf
Info) Analyzing structure ...
Info) Atoms: 1231
Info) Residues: 76
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
Info) Using plugin pdb for coordinates from file ubq.pdb
Info) Finished with coordinate file ubq.pdb.
reading structure from psf file ubq.psf
PSF file is in CHARMM format; XPLOR format required.
error reading atoms
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
So I dont know where the error is. Does Solvate accept CHARMM files?
or my problem comes from other source??? writing "package require
solvate" and then "solvate" don't show any option to specify which PSF
format will be used. Can someone give a hand???
Thanks a lot
Leonardo
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