From: DimitryASuplatov (genesup_at_gmail.com)
Date: Thu Apr 30 2009 - 05:23:31 CDT
Hello,
I am trying to run EM on my system. In response from NAMD I receive
this:
========================================================================
PRESSURE: 0 nan nan nan nan nan nan nan nan nan
GPRESSURE: 0 nan nan nan nan nan nan nan nan nan
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP TOTAL2 TOTAL3
TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG
GPRESSAVG
ENERGY: 0 29188.5684 11280.9318 2173.8717
56.3938 -307666.8998 99999999.9999 0.0000 0.0000
0.0000 99999999.9999 0.0000 99999999.9999 99999999.9999
0.0000 -99999999.9999 -99999999.9999 1031138.3094 -99999999.9999
-99999999.9999
OPENING EXTENDED SYSTEM TRAJECTORY FILE
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: nan
BRACKET: 0 0 nan nan nan
BRACKET: 0 0 nan nan nan
========================================================================
Ive searched the mail list and found that letter with the same problem.
To my understanding this happens when the structure is too far from
optimal. For example, when atoms were guessed incorrectly by PSF. To my
understanding this should be a VERY incorrect guess or multiple copies
of it. Ive looked at my structure and did not find anything except for
some strange angles for proline hydrogens, though I would not take it to
be a big problem.
My questions are:
1/ What is the general procedure to tackle such kind of problems? It is
not cool to check each and every atom and angle in my structure. What
residues are more likely to cause the problem?
2/ Can I set some kind of more verbose output to see the atom number
with the highest energy which most likely cause the problem?
3/ Can I use more advanced em algorythm in namd to avoid this clash?
My psfgen output follows. I do not paste psfgen options and em.conf file
since they work perfectly in all other cases.
Thank you for your time
SDA
INFO: Preparing structure for energy minimization
Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info) Free system memory: 27183MB (84%)
Kluyvera_citrophila.nowater.B99990014.pdb
1klc.opt.charmm.tip3
15
Info) Using plugin pdb for structure file
Kluyvera_citrophila.nowater.B99990014.pdb
Info) Using plugin pdb for coordinates from file
Kluyvera_citrophila.nowater.B99990014.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file
Kluyvera_citrophila.nowater.B99990014.pdb.
Info) Analyzing structure ...
Info) Atoms: 6034
Info) Bonds: 6202
Info) Residues: 765
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 3 Protein: 2 Nucleic: 0
0
atomselect0
Info) Opened coordinate file 1klc.opt.charmm.tip3_notprotein.pdb for
writing.
Info) Finished with coordinate file 1klc.opt.charmm.tip3_notprotein.pdb.
atomselect1
1 0
Info) Opened coordinate file 1klc.opt.charmm.tip3_1.pdb for writing.
Info) Opened coordinate file 1klc.opt.charmm.tip3_0.pdb for writing.
Info) Finished with coordinate file 1klc.opt.charmm.tip3_1.pdb.
Info) Finished with coordinate file 1klc.opt.charmm.tip3_0.pdb.
1.4.5
reading topology file top_all27_prot_lipid.inp
> CHARMM22 All-Hydrogen Topology File for Proteins and Lipids <<
>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
>>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<<
All comments to ADM jr. via the CHARMM web site: www.charmm.org
parameter set discussion forum
Created by CHARMM version 31 1
cross-term entries present in topology definitions
aliasing residue ILE atom CD1 to CD
aliasing residue SER atom HG to HG1
aliasing residue HIS to HSD
aliasing residue CA atom CA to CAL
aliasing residue CA to CAL
aliasing residue K to POT
aliasing residue K atom K to POT
aliasing residue ICL to CLA
aliasing residue ICL atom CL to CLA
aliasing residue INA to SOD
aliasing residue INA atom NA to SOD
aliasing residue LYS atom 1HZ to HZ1
aliasing residue LYS atom 2HZ to HZ2
aliasing residue LYS atom 3HZ to HZ3
aliasing residue ARG atom 1HH1 to HH11
aliasing residue ARG atom 2HH1 to HH12
aliasing residue ARG atom 1HH2 to HH21
aliasing residue ARG atom 2HH2 to HH22
aliasing residue ASN atom 1HD2 to HD21
aliasing residue ASN atom 2HD2 to HD22
aliasing residue G to GUA
aliasing residue C to CYT
aliasing residue A to ADE
aliasing residue T to THY
aliasing residue U to URA
aliasing residue HOH atom O to OH2
aliasing residue HOH to TIP3
building segment 1
reading residues from pdb file 1klc.opt.charmm.tip3_1.pdb
extracted 209 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N 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 cross-term C-N-CA-C-N-CA-C-N 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.
reading coordinates from pdb file 1klc.opt.charmm.tip3_1.pdb for segment
1
Warning: failed to set coordinate for atom O ALA:209 1
Warning: failed to set coordinate for atom OXT ALA:209 1
building segment 0
setting patch for first residue to NNEU
reading residues from pdb file 1klc.opt.charmm.tip3_0.pdb
extracted 555 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N 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 cross-term C-N-CA-C-N-CA-C-N 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.
reading coordinates from pdb file 1klc.opt.charmm.tip3_0.pdb for segment
0
Warning: failed to set coordinate for atom O ARG:764 0
Warning: failed to set coordinate for atom OXT ARG:764 0
building segment NPR
reading residues from pdb file 1klc.opt.charmm.tip3_notprotein.pdb
extracted 1 residues from pdb file
Info: generating structure...
Info: segment complete.
reading coordinates from pdb file 1klc.opt.charmm.tip3_notprotein.pdb
for segment NPR
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
applying patch DISU to 2 residues
Info: guessing coordinates for 5812 atoms (13 non-hydrogen)
Warning: poorly guessed coordinates for 9 atoms (4 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 ALA:1 1
Warning: poorly guessed coordinate for atom HT2 ALA:1 1
Warning: poorly guessed coordinate for atom HT3 ALA:1 1
Warning: poorly guessed coordinate for atom OT1 ALA:209 1
Warning: poorly guessed coordinate for atom OT2 ALA:209 1
Warning: poorly guessed coordinate for atom HT1 SER:210 0
Warning: poorly guessed coordinate for atom HT2 SER:210 0
Warning: poorly guessed coordinate for atom OT1 ARG:764 0
Warning: poorly guessed coordinate for atom OT2 ARG:764 0
Warning: failed to guess coordinates for 9 atoms
Info: writing pdb file 1klc.opt.charmm.tip3.vac.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
Info: writing psf file 1klc.opt.charmm.tip3.vac.psf
total of 11842 atoms
total of 12005 bonds
total of 21633 angles
total of 31831 dihedrals
total of 2031 impropers
total of 760 cross-terms
Info: psf file complete.
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