RE: Unable to Generate PSF file !

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Jul 04 2005 - 10:06:46 CDT

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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