RE: Unable to Generate PSF file !

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Jul 04 2005 - 11:42:44 CDT

You're missing two key lines before you can write out the psf and pdb.

segment A {pdb hexane.pdb}
coordpdb hexane.pdb A

See the namd tutorial and psfgen manual for more details.

-----Original Message-----
From: Tamal Banerjee [mailto:tamal_at_iitk.ac.in]
Sent: Monday, July 04, 2005 11:35 AM
To: JC Gumbart
Subject: RE: namd-l: Unable to Generate PSF file !

I have opened the tkconsole menu of VMD.
and typed the following lines:

package require psfgen
topology hexane.inp
writepdb ubq.pdb
writepsf ubq.psf

thanks,

Tamal

> Please list the exact commands you are using to generate the psf.
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> Of Tamal Banerjee
> Sent: Monday, July 04, 2005 8:10 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Unable to Generate PSF file !
>
> I am a beginner for this NAMD package.
> I have sucessfully ran the 1st Tutorial i.e the 1-1 build directory for
> ubliquitin.But when I tried that on a simple molecule like hexane I was
> unable to generate the psf file.The pdb file and the topology file are
> given below.
>
> pdb file for hexane:
>
> ATOM 1 C1 HEX 1 -1.374 0.001 -2.632 1.00
> ATOM 2 C2 HEX 1 -1.374 0.001 -1.182 1.00
> ATOM 3 C3 HEX 1 -0.007 0.001 -0.699 1.00
> ATOM 4 C4 HEX 1 -0.007 0.001 0.751 1.00
> ATOM 5 C5 HEX 1 1.360 0.001 1.235 1.00
> ATOM 6 C6 HEX 1 1.360 0.001 2.685 1.00
> ATOM 7 H6A HEX 1 2.387 0.001 3.048 1.00
> ATOM 8 H6B HEX 1 0.675 0.001 3.532 1.00
> ATOM 9 H6C HEX 1 1.077 1.013 2.395 1.00
> ATOM 10 H5A HEX 1 1.873 -0.888 0.872 1.00
> ATOM 11 H5B HEX 1 1.485 0.811 0.517 1.00
> ATOM 12 H4A HEX 1 -0.241 -0.973 0.324 1.00
> ATOM 13 H4B HEX 1 -0.521 0.891 1.114 1.00
> ATOM 14 H3A HEX 1 1.019 0.001 -1.062 1.00
> ATOM 15 H3B HEX 1 0.233 1.000 -1.062 1.00
> ATOM 16 H2A HEX 1 -2.059 0.001 -0.335 1.00
> ATOM 17 H2B HEX 1 -1.374 -1.025 -0.819 1.00
> ATOM 18 H1A HEX 1 -0.348 0.001 -2.995 1.00
> ATOM 19 H1B HEX 1 -2.059 0.001 -3.479 1.00
> ATOM 20 H1C HEX 1 -1.888 -0.888 -2.995 1.00
>
>
> Topology file( hexane.inp):
>
> 27 1
> MASS 1 HA 1.008 H !BONDED TO METHYL GROUPS
> MASS 2 CT3 12.011 C! METHYL CARBON
> MASS 3 HB 1.008 H ! BONDED TO METHYLENE GROUP
> MASS 4 CT2 12.011 C ! METHYLENE CARBON
>
> RESI HEX 0.00 ! HEXANE
> GROUP
> ATOM H1A HA -0.03
> ATOM H1B HA -0.03
> ATOM H1C HA -0.03
> ATOM C1 CT3 0.09
> GROUP
> ATOM H2A HB -0.03
> ATOM H2B HB -0.03
> ATOM C2 CT2 0.06
> GROUP
> ATOM H3A HB -0.03
> ATOM H3B HB -0.03
> ATOM C3 CT2 0.06
> GROUP
> ATOM H4A HB -0.03
> ATOM H4B HB -0.03
> ATOM C4 CT2 0.06
> GROUP
> ATOM H5A HB -0.03
> ATOM H5B HB -0.03
> ATOM C5 CT2 0.06
> GROUP
> ATOM H6A HA -0.03
> ATOM H6B HA -0.03
> ATOM H6C HA -0.03
> ATOM C6 CT3 0.09
> BOND H1A C1 H1B C1 H1C C1 C2 C1
> BOND H2A C2 H2B C2 C3 C2
> BOND H3A C3 H3B C3 C4 C3
> BOND H4A C4 H4B C4 C5 C4
> BOND H5A C5 H5B C5 C6 C5
> BOND H6A C6 H6B C6 H6C C6
> IMPR C1 H1A H1B H1C
> IMPR C2 C1 H2A H2B
> IMPR C3 C2 H3A H3B
> IMPR C4 C3 H4A H4B
> IMPR C5 C4 H5A H5B
> IMPR C6 C5 H6A H6B
> PATCH FIRST NONE LAST NONE
>
> When we tried to generate the psf file on VMD 1.8.2,it was reading the
> topology file but not generating any data inside the psf file.
> Kindly suggest the possible solution.
>
> thanks
>
> Tamal
>
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