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From: Rudra Banerjee (bnrj.rudra_at_yahoo.com)
Date: Thu Sep 18 2008 - 03:29:07 CDT
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dear irene,
thanks for youre reply. let me send the psfgen ,log and corresponding output.
my psfgen file is:
package require psfgen
topology my-top.inp
segment U {pdb ao_tst.pdb}
coordpdb ao_tst.pdb U
guesscoord
writepdb aoq.pdb
writepsf aoq.psf
the psfgen log file is:
reading topology file my-top.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
ERROR! Failed to parse improper statement.
building segment U
reading residues from pdb file ao_tst.pdb
extracted 1 residues from pdb file
Info: generating structure...
no atom C in residue MAC:A 1 of segment U
Warning: add conformation failed in patch NTER
U:A 1
U:A 1
Info: segment complete.
reading coordinates from pdb file ao_tst.pdb for segment U
Warning: failed to set coordinate for atom NR2 MAC:A 1 U
Warning: failed to set coordinate for atom NH2 MAC:A 1 U
Warning: failed to set coordinate for atom NH2 MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Warning: failed to set coordinate for atom HP MAC:A 1 U
Info: guessing coordinates for 45 atoms (22 non-hydrogen)
Warning: poorly guessed coordinates for 4 atoms (1 non-hydrogen):
Warning: poorly guessed coordinate for atom N2 MAC:A 1 U
Warning: poorly guessed coordinate for atom HA1 MAC:A 1 U
Warning: poorly guessed coordinate for atom HA2 MAC:A 1 U
Warning: poorly guessed coordinate for atom HA3 MAC:A 1 U
Warning: failed to guess coordinates for 41 atoms
Info: writing pdb file aoq.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
Info: writing psf file aoq.psf
total of 46 atoms
total of 43 bonds
total of 72 angles
total of 77 dihedrals
total of 1 impropers
total of 0 cross-terms
Info: psf file complete.
vmd >
and the correspondingpdb output(aoq.pdb) is:
REMARK original generated coordinate pdb file
ATOM 1 C MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 2 OT1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U O
ATOM 3 OT2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U O
ATOM 4 N MAC 0 0.000 0.000 0.000 -1.00 0.00 U N
ATOM 5 HT1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 6 HT2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 7 HT3 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 8 CA MAC 0 4.407 -3.273 0.925 1.00 0.00 U C
ATOM 9 HA MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 10 N2 MAC 0 5.407 -3.273 0.925 0.00 0.00 U N
ATOM 11 HA1 MAC 0 4.081 -2.327 0.925 0.00 0.00 U H
ATOM 12 HA2 MAC 0 4.070 -3.746 0.111 0.00 0.00 U H
ATOM 13 HA3 MAC 0 4.070 -3.746 1.739 0.00 0.00 U H
ATOM 14 CB MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 15 HB1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 16 HB2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 17 HB3 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 18 CD1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 19 HD1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 20 CE1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 21 HE1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 22 CZ MAC 0 0.000 0..000 0.000 -1.00 0.00 U C
ATOM 23 CG MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 24 CD2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 25 HD2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 26 CE2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 27 C1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 28 H1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 29 C2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 30 C3 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 31 C4 MAC 0 0.000 0.000 0.000 -1.00 0..00 U C
ATOM 32 H4 MAC 0 0.000 0.000 0.000 -1..00 0.00 U H
ATOM 33 C5 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 34 H5 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 35 C7 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 36 H7 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 37 C6 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 38 N1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U N
ATOM 39 C8 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 40 C9 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C
ATOM 41 H81 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 42 H82 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 43 H83 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 44 H91 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 45 H92 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
ATOM 46 H93 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H
END
here you can see that output pdb differs from the input pdb.i have no clue why.plz help
-- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu.org/philosophy/no-word-attachments.html ----- Original Message ---- From: Rudra Banerjee <bnrj..rudra_at_yahoo.com> To: Irene Newhouse <einew_at_hotmail.com> Sent: Thursday, 18 September, 2008 1:51:53 PM Subject: Re: vmd-l: problem with psf file generation REMARK original generated coordinate pdb file ATOM 1 C MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 2 OT1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U O ATOM 3 OT2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U O ATOM 4 N MAC 0 0.000 0.000 0.000 -1.00 0.00 U N ATOM 5 HT1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 6 HT2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 7 HT3 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 8 CA MAC 0 4.407 -3..273 0.925 1.00 0.00 U C ATOM 9 HA MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 10 N2 MAC 0 5.407 -3.273 0.925 0.00 0.00 U N ATOM 11 HA1 MAC 0 4.081 -2.327 0.925 0.00 0.00 U H ATOM 12 HA2 MAC 0 4.070 -3.746 0.111 0.00 0.00 U H ATOM 13 HA3 MAC 0 4.070 -3.746 1.739 0.00 0.00 U H ATOM 14 CB MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 15 HB1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 16 HB2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 17 HB3 MAC 0 0.000 0.000 0.000 -1.00 0..00 U H ATOM 18 CD1 MAC 0 0.000 0.000 0.000 -1..00 0.00 U C ATOM 19 HD1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 20 CE1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 21 HE1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 22 CZ MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 23 CG MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 24 CD2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 25 HD2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 26 CE2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 27 C1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 28 H1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 29 C2 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 30 C3 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 31 C4 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 32 H4 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 33 C5 MAC 0 0.000 0..000 0.000 -1.00 0.00 U C ATOM 34 H5 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 35 C7 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 36 H7 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 37 C6 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 38 N1 MAC 0 0.000 0.000 0.000 -1.00 0.00 U N ATOM 39 C8 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 40 C9 MAC 0 0.000 0.000 0.000 -1.00 0.00 U C ATOM 41 H81 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 42 H82 MAC 0 0.000 0.000 0.000 -1.00 0..00 U H ATOM 43 H83 MAC 0 0.000 0.000 0.000 -1..00 0.00 U H ATOM 44 H91 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 45 H92 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H ATOM 46 H93 MAC 0 0.000 0.000 0.000 -1.00 0.00 U H END here you can see the difference between my original and generated pdb file. plz help Get an email ID as yourname_at_ymail.com or yourname_at_rocketmail.com. Click here http://in.promos.yahoo.com/address Be the first one to try the new Messenger 9 Beta! Go to http://in.messenger.yahoo.com/win/
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