[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.


*****************************************.
.
.
.
.
.
; 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
.
.
.
.
.

***********************************************************************************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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