From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed May 04 2005 - 17:17:01 CDT
Hi,
That's okay. The problem with psfgen is that it doesn't read the stream
files as you can do using CHARMM. But if you just CAREFULLY copy and
paste the topology and parameters of the HEM group, then the simulation
should be okay. Just one thing, as pointed by Alex McKerell and Charles
Brooks, you should handle with care those "modified" files, since you
can "contaminate" the parent files and you might have serious problems
in future.
On the other hand, Surendra, I guess you have to enable the angle and
dihedral autogeneration when building the HEM using psfgen. Is the only
thing I can say after checking your log file.
Enjoy!
Peace,
Michel
-----Original Message-----
From: Peter Bazeley [mailto:petebazeley_at_yahoo.com]
Sent: Wednesday, May 04, 2005 5:05 PM
To: Michel Espinoza-Fonseca
Subject: RE: namd-l: NAMD: HEM residue
Hi Surendra
Are you using CHARMM? I ran into this problem as well.
I used top_all22_prot.inp to build the protein segment
and toppar_all22_prot_heme.str (in the stream
directory) to build the heme segment. I don't think
this is the proper way, but it worked.
Pete
--- Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>
wrote:
> Could you provide us your input file, please?
> Cheers,
> Michel
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu
> [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf Of surendra negi
> Sent: Wednesday, May 04, 2005 2:57 PM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: NAMD: HEM residue
>
> Hi All,
> I am trying to create a psf file from PDB. My PDB
> file has both HOH and HEM entry. The script I wrote
> is
> running file till HOH. But it is unable to guess
> coordinate for HEM. Here is the log file generated
> by
> NAMD. Thanks a lot for help or suggestions.
> Regards
> surendra
> ----------LOG FILE-------
> reading residues from pdb file
> output/test_protein.pdb
> extracted 465 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.
> *** writing psf structure file ***
> Info: writing psf file output/test.psf
> total of 7479 atoms
> total of 7573 bonds
> total of 13693 angles
> total of 20147 dihedrals
> total of 1218 impropers
> Info: psf file complete.
>
> *** guessing missing coordinates ***
> Info: guessing coordinates for 3748 atoms (2
> non-hydrogen)
> Warning: poorly guessed coordinates for 5 atoms (2
> non-hydrogen):
> Warning: poorly guessed coordinate for atom HT1
> GLY:28 XPRT
> Warning: poorly guessed coordinate for atom HT2
> GLY:28 XPRT
> Warning: poorly guessed coordinate for atom HT3
> GLY:28 XPRT
> Warning: poorly guessed coordinate for atom OT1
> HSE:492 XPRT
> Warning: poorly guessed coordinate for atom OT2
> HSE:492 XPRT
> *** writing pdb coordinate file ***
> Info: writing pdb file output/test.pdb
> Info: Atoms with guessed coordinates will have
> occupancy of 0.0.
> Info: pdb file complete.
> *** advanced demo begins here ***
> *** adding a segment of water ***
> aliasing residue HOH to TIP3
> building segment SOLV
> disabling angle autogeneration
> disabling dihedral autogeneration
> reading residues from pdb file output/test_water.pdb
> extracted 261 residues from pdb file
> Info: generating structure...
> Info: segment complete.
> *** reading water coordinates ***
> aliasing residue HOH atom O to OH2
>
> *** guessing missing coordinates ***
> Info: guessing coordinates for 3748 atoms (2
> non-hydrogen)
> Warning: poorly guessed coordinates for 5 atoms (2
> non-hydrogen):
> Warning: poorly guessed coordinate for atom HT1
> GLY:28 XPRT
> Warning: poorly guessed coordinate for atom HT2
> GLY:28 XPRT
> Warning: poorly guessed coordinate for atom HT3
> GLY:28 XPRT
> Warning: poorly guessed coordinate for atom OT1
> HSE:492 XPRT
> Warning: poorly guessed coordinate for atom OT2
> HSE:492 XPRT
> *** writing pdb coordinate file ***
> Info: writing pdb file output/test.pdb
> Info: Atoms with guessed coordinates will have
> occupancy of 0.0.
> Info: pdb file complete.
> *** advanced demo begins here ***
> *** adding a segment of water ***
> aliasing residue HOH to TIP3
> building segment SOLV
> disabling angle autogeneration
> disabling dihedral autogeneration
> reading residues from pdb file output/test_water.pdb
> extracted 261 residues from pdb file
> Info: generating structure...
> Info: segment complete.
> *** reading water coordinates ***
> aliasing residue HOH atom O to OH2
> ...
> ...
> ...
> Warning: failed to set coordinate for atom O1D
> HEM:500 HEM
> Warning: failed to set coordinate for atom O2D
> HEM:500 HEM
> *** guessing HEM coordinates - not possible ***
> ERROR: failed on guessing coordinates
>
>
>
>
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