Re: tmao molecule

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed May 20 2009 - 09:51:43 CDT

You need to define the start of a segment using the segment command...
have a look at the sections of the namd tutorial that involve generation
of psfs.
Best,
Peter

Vasudevan V wrote:
> Hello,
>
> I am a new user of namd and I am trying to create a tmao molecule. I
> did the following steps but nothing gets written into my psf and i do
> not get any explicit error message also. My pdb contains exactly one
> molecule of tmao with Hydrogen atoms explicitly definied.
>
>
> I added the following definition to the topology
>
> RESI TMA 0.000 !
> GROUP
> ATOM N1 NTL 0.440
> ATOM O2 NO -0.650
> ATOM C3 CTL3 -0.260
> ATOM C4 CTL3 -0.260
> ATOM C5 CTL3 -0.260
> ATOM H6 HAL3 0.110
> ATOM H7 HAL3 0.110
> ATOM H8 HAL3 0.110
> ATOM H9 HAL3 0.110
> ATOM H10 HAL3 0.110
> ATOM H11 HAL3 0.110
> ATOM H12 HAL3 0.110
> ATOM H13 HAL3 0.110
> ATOM H14 HAL3 0.110
> BOND N1 O2 N1 C3 N1 C4 N1 C5
> BOND C3 H6 C3 H7 C3 H8
> BOND C4 H9 C4 H10 C4 H11
> BOND C5 H12 C5 H13 C5 H14
>
> and I have defined the bond and angle parameters for the NO bond in
> the parameter file.
>
> NO NTL 347.564 1.4070 ! TMAO Nitrogen Oxygen
>
> and the pgn file i use to generate is as follows
>
> package require psfgen
> topology top_tmao.inp
> coordpdb tmao_namd.pdb
> writepdb tma.pdb
> writepsf tma.psf
>
> but there are no atoms being written into the psf file which i
> generate. The output of the script is
>
> 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
> <mailto: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, 2 CPUs detected.
> Info) Free system memory: 3450MB (88%)
> 1.4.5
> reading topology file top_tmao.inp
>
> >>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
> >>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
> from
> >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
> >>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
> >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu
> <http://mmiris.ab.umd.edu> <<<<<<<<<
> and
> \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
> \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
> Alexander D. MacKerell Jr.
> August 1999
> All comments to ADM jr. email: alex,mmiris.ab.umd.edu
> <http://mmiris.ab.umd.edu>
> telephone: 410-706-7442
>
> Created by CHARMM version 27 1
> Info: writing pdb file tma.pdb
> Info: pdb file complete.
> Info: writing psf file tma.psf
> total of 0 atoms
> total of 0 bonds
> total of 0 angles
> total of 0 dihedrals
> total of 0 impropers
> total of 0 cross-terms
> Info: psf file complete.
>
>

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