Re: tmao molecule

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed May 20 2009 - 10:13:29 CDT

Ah, that's because your topology tells psfgen to apply the patches NTER
and CTER (there's probably an AUTO line in there somewhere), but your
topology file doesn't actually have those patches. Try replacing that
segment command with

segment T {
    pdb tmao_namd.pdb
    first NONE
    last NONE
}

or remove the automatic patching line from your topology.

BTW, please reply to the list so that the discussion is archived.
Best,
Peter

Vasudevan V wrote:
> I tried the segment command.
>
> segment T{pdb tmao_namd.pdb}
>
> It gives the following message
>
> unknown patch type NTER
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> MOLECULE MISSING! Use resetpsf to start over.
>
>
>
> On Wed, May 20, 2009 at 10:51 AM, Peter Freddolino
> <petefred_at_ks.uiuc.edu <mailto:petefred_at_ks.uiuc.edu>> wrote:
>
> 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> <mailto: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> <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> <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.
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:00 CST