[gmx-users] problem with pdb2gmx to generate top file
Moeed
lecielll at googlemail.com
Sun May 9 16:59:58 CEST 2010
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.
*****************************************.
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; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove propers over the same bond as an improper if it is 1
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 3 1 1 3 1 0
[ HEX ]
[ atoms ]
C1 opls_157 -0.180 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
H13 opls_140 0.060 1
C2 opls_158 -0.120 2
H21 opls_140 0.060 2
H22 opls_140 0.060 2
C3 opls_158 0.120 3
H31 opls_140 0.060 3
H32 opls_140 0.060 3
C4 opls_158 -0.120 4
H41 opls_140 0.060 4
H42 opls_140 0.060 4
C5 opls_158 -0.120 5
H51 opls_140 0.060 5
H52 opls_140 0.060 5
C6 opls_157 -0.180 6
H61 opls_140 0.060 6
H62 opls_140 0.060 6
H63 opls_140 0.060 6
[ bonds ]
C1 H11
C1 H12
C1 H13
C1 C2
C2 H21
C2 H22
C2 C3
C3 H31
C3 H32
C3 C4
C4 H41
C4 H42
C4 C5
C5 H51
[ ACE ]
[ atoms ]
CH3 opls_135 -0.180 1
HH31 opls_140 0.060 1
HH32 opls_140 0.060 1
HH33 opls_140 0.060 1
C opls_235 0.500 2
O opls_236 -0.500 2
[ bonds ]
CH3 HH31
CH3 HH32
CH3 HH33
CH3 C
C O
[ impropers ]
CH3 +N C O improper_O_C_X_Y
[ ALA ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_135 -0.180 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
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***********************************************************************************commans
I type in:
pdb2gmx -f Hexane-PRODRG.pdb -o Hexane-PRODRG.gro -p Hexane-PRODRG.top -ff
oplsaa >& output.pdb2gmx
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
************************************************************************************************
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