From: Vasudevan V (vasu.chemical_at_gmail.com)
Date: Wed May 20 2009 - 10:19:45 CDT
Hi Peter
Thanks a lot, that did the trick,
I actually tried the first none command. Is the command case sensitive?
because in the tutorial everything was lower case, that gave me some error
but when I use the upper case as you had written it worked.
Regards
vasu
On Wed, May 20, 2009 at 11:13 AM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:
> 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.
>>
>>
>>
>>
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