Moeed wrote:
Hello,
I am trying to generate gro and top file with pdb2gmx program. I have
made a copy of ffoplsaa.rtp from library to working directory and added
Hexane molecule residue to the beginning of the ffoplsaa.rtp.
<snip>
I type in:
pdb2gmx -f Hexane-PRODRG.pdb -o Hexane-PRODRG.gro -p Hexane-PRODRG.top
-ff oplsaa >& output.pdb2gmx
In principal, this should work, but if it's not, then stop redirecting your
output (i.e., let it print to the screen) and see what pdb2gmx is doing.
Otherwise, inspect this "output.pdb2gmx" for error messages, etc.
-Justin
I do not get gro file at all and top file I get contains the following
comments only!:
;********************************************************************
; File 'Hexane-PRODRG.top' was generated
; By user: moeed (500)
; On host: moeed-desktop
; At date: Sun May 9 10:47:26 2010
;
; This is your topology file
; "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)
;
; Include forcefield parameters
#include "ffoplsaa.itp"
***************************************
***************Hexane-PRODRG.pdb
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 C1 HEX 1 8.330 1.510 -0.010 0.00
0.00 C
ATOM 2 H11 HEX 1 9.281 1.200 -0.024 0.00
0.00 H
ATOM 3 H12 HEX 1 8.154 2.080 -0.813 0.00
0.00 H
ATOM 4 H13 HEX 1 8.166 2.044 0.820 0.00
0.00 H
ATOM 5 C2 HEX 1 7.400 0.300 -0.030 0.00
0.00 C
ATOM 6 H21 HEX 1 7.584 -0.267 0.773 0.00
0.00 H
ATOM 7 H22 HEX 1 7.573 -0.231 -0.860 0.00
0.00 H
ATOM 8 C3 HEX 1 5.940 0.730 -0.010 0.00
0.00 C
ATOM 9 H31 HEX 1 5.754 1.291 -0.816 0.00
0.00 H
ATOM 10 H32 HEX 1 5.769 1.266 0.817 0.00
0.00 H
ATOM 11 C4 HEX 1 5.010 -0.480 -0.020 0.00
0.00 C
ATOM 12 H41 HEX 1 5.192 -1.038 0.790 0.00
0.00 H
ATOM 13 H42 HEX 1 5.186 -1.020 -0.843 0.00
0.00 H
ATOM 14 C5 HEX 1 3.540 -0.050 -0.010 0.00
0.00 C
ATOM 15 H51 HEX 1 3.357 0.507 -0.820 0.00
0.00 H
ATOM 16 H52 HEX 1 3.363 0.489 0.813 0.00
0.00 H
ATOM 17 C6 HEX 1 2.610 -1.270 -0.020 0.00
0.00 C
ATOM 18 H61 HEX 1 1.658 -0.964 -0.013 0.00
0.00 H
ATOM 19 H62 HEX 1 2.780 -1.812 -0.843 0.00
0.00 H
ATOM 20 H63 HEX 1 2.785 -1.830 0.790 0.00
0.00 H
END
************************************************************************************************
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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