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From: Sebastian Maximilian Wilhelm (Sebastian.Wilhelm_at_rwth-aachen.de)
Date: Fri Feb 25 2011 - 05:30:45 CST

Hi,

I tried to write my own topo-file for a methanol TOPMethanol.inp:

* Topology file for Methanol
*
*
MASS 1 CH3 15.03500 CH3 ! site CH3
MASS 2 OS 15.99900 O ! hydroxyl oxygen
MASS 3 HS 1.00800 H ! hydroxyl hydrogen

RESI ME 0.00
AUTO ANGLES !
                          !
GROUP
                          ! C3--O
ATOM C3 CH3 0.32 ! \
ATOM O OS -0.66 ! H
ATOM H HS 0.34
BOND C3 O O H

END

I´ve read that it is not absolute essential to write the ICs if all molecules and their positions are available from the .pdb-file. I have converted a .pdb-file for the trajectories (400 frames) of 4 methanol molecules (Methanol1234.pdb):

CRYST1 64.750 64.750 64.750 90.00 90.00 90.00 P 1 1
ATOM 1 C3 ME X 1 4.876 -24.666 -17.653 0.00 0.00
ATOM 2 O ME X 1 4.114 -25.506 -18.524 0.00 0.00
ATOM 3 H ME X 1 3.287 -25.047 -18.532 0.00 0.00
ATOM 4 C3 ME X 2 2.657 -3.561 -14.849 0.00 0.00
ATOM 5 O ME X 2 2.210 -4.727 -15.547 0.00 0.00
ATOM 6 H ME X 2 2.414 -4.630 -16.465 0.00 0.00
ATOM 7 C3 ME X 3 -18.595 28.600 -32.029 0.00 0.00
ATOM 8 O ME X 3 -17.593 27.584 -31.955 0.00 0.00
ATOM 9 H ME X 3 -17.643 27.227 -31.081 0.00 0.00
ATOM 10 C3 ME X 4 -29.535 -26.831 -25.221 0.00 0.00
ATOM 11 O ME X 4 -29.762 -26.388 -23.880 0.00 0.00
ATOM 12 H ME X 4 -29.500 -27.099 -23.316 0.00 0.00
END
(my comment: next frame)
ATOM 1 C3 ME X 1 4.875 -24.695 -17.615 0.00 0.00
ATOM 2 O ME X 1 4.118 -25.488 -18.534 0.00 0.00
ATOM 3 H ME X 1 3.295 -25.025 -18.509 0.00 0.00
ATOM 4 C3 ME X 2 2.657 -3.566 -14.850 0.00 0.00
ATOM 5 O ME X 2 2.234 -4.733 -15.559 0.00 0.00
ATOM 6 H ME X 2 2.428 -4.601 -16.475 0.00 0.00
ATOM 7 C3 ME X 3 -18.614 28.585 -32.030 0.00 0.00
ATOM 8 O ME X 3 -17.576 27.603 -31.968 0.00 0.00
ATOM 9 H ME X 3 -17.584 27.244 -31.094 0.00 0.00
ATOM 10 C3 ME X 4 -29.531 -26.845 -25.227 0.00 0.00
ATOM 11 O ME X 4 -29.757 -26.391 -23.891 0.00 0.00
ATOM 12 H ME X 4 -29.458 -27.060 -23.294 0.00 0.00
END
.
.
.

and the script out of the NAMD tutorial for creating .psf adapted to my specifications:

package require psfgen
topology TOPMethanol.inp
segment Al {pdb Methanol1234.pdb}
coordpdb Methanol1234.pdb Al
writepdb PDBMethanol.pdb
writepsf PSFMethanol.psf

If I execute this script in the VMD Tk console, four warnings occur: failed to set coordinate for atom C3 in ME1, ME2, ME3, ME4. Anyway, the .pdb and the .psf files are written, but in the PDBMethanol.pdb-file no coordinates for C3 are entered:

REMARK original generated coordinate pdb file
ATOM 1 O ME X 1 4.114 -25.506 -18.524 1.00 0.00 AL O
ATOM 2 H ME X 1 3.287 -25.047 -18.532 1.00 0.00 AL H
ATOM 3 O ME X 2 2.210 -4.727 -15.547 1.00 0.00 AL O
ATOM 4 H ME X 2 2.414 -4.630 -16.465 1.00 0.00 AL H
ATOM 5 O ME X 3 -17.593 27.584 -31.955 1.00 0.00 AL O
ATOM 6 H ME X 3 -17.643 27.227 -31.081 1.00 0.00 AL H
ATOM 7 O ME X 4 -29.762 -26.388 -23.880 1.00 0.00 AL O
ATOM 8 H ME X 4 -29.500 -27.099 -23.316 1.00 0.00 AL H
END

and in the .psf-file, no C3 occurs:
PSF

       3 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS topology TOPMethanol.inp
 REMARKS segment AL { first NONE; last NONE; auto angles }

       8 !NATOM
       1 AL 1 ME O OS -0.660000 15.9990 0
       2 AL 1 ME H HS 0.340000 1.0080 0
       3 AL 2 ME O OS -0.660000 15.9990 0
       4 AL 2 ME H HS 0.340000 1.0080 0
       5 AL 3 ME O OS -0.660000 15.9990 0
       6 AL 3 ME H HS 0.340000 1.0080 0
       7 AL 4 ME O OS -0.660000 15.9990 0
       8 AL 4 ME H HS 0.340000 1.0080 0

       0 !NBOND: bonds

       0 !NTHETA: angles

       0 !NPHI: dihedrals
Now, I have two questions:
-why is C3 ignored? I tried changing the name into CH3, only C or even totally different like A1 (of course in the original .pdb and in the topology-file), but nothing has changed.
-why is only one frame instead of 400 written?

Thanks for your help!

Best regards,
Sebastian