[gmx-users] Generating topology with pdb2gmx
Moeed
lecielll at googlemail.com
Sun May 9 00:36:20 CEST 2010
Dear Justin,
1- Unfortunately, I am having difficulty running the simple program pdb2gmx
with pdb file you sent me for Hexane.. I have in working directory pdb file
and rtp files:
Hexane-PRODRG.pdb rtp.pdb
pdb2gmx -f Hexane-PRODRG.pdb -o Hexane.gro -p Hexane.top >& output.pdb2gmx
output.pdb2gmx says:
Opening library file /chem_soft/gromacs/share/gromacs/top/FF.dat
2-can you please tell me why I need rtp file? previously I just created pdb
file and used x2top an dI had no rtp file...
Thank you for your help.
******************************************************************
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
*******************************rtp.pdb :
[ 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
C5 H52
C5 C6
C6 H61
C6 H62
C6 H63
****************************************************************************************Also
I have tried x2top comamnd: x2top -f Hexane-PRODRG.pdb -o Hexane.top -alldih
-ff oplsaa -name HEX
as you suggested I am using -alldih flag to generate all dihedrals
Option Filename Type Description
------------------------------------------------------------
-f Hexane-PRODRG.pdb Input Structure file: gro g96 pdb tpr tpb tpa
-o Hexane.top Output, Opt! Topology file
-r out.rtp Output, Opt. Residue Type file used by pdb2gmx
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-ff string oplsaa Force field for your simulation. Type "select"
for interactive selcection.
-[no]v bool no Generate verbose output in the top file.
-nexcl int 3 Number of exclusions
-[no]H14 bool yes Use 3rd neighbour interactions for hydrogen
atoms
-[no]alldih bool yes Generate all proper dihedrals
-[no]remdih bool no Remove dihedrals on the same bond as an improper
-[no]pairs bool yes Output 1-4 interactions (pairs) in topology file
-name string HEX Name of your molecule
-[no]pbc bool yes Use periodic boundary conditions.
-[no]pdbq bool no Use the B-factor supplied in a pdb file for the
atomic charges
-[no]param bool yes Print parameters in the output
-[no]round bool yes Round off measured values
-kb real 400000 Bonded force constant (kJ/mol/nm^2)
-kt real 400 Angle force constant (kJ/mol/rad^2)
-kp real 5 Dihedral angle force constant (kJ/mol/rad^2)
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /chem_soft/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /chem_soft/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /chem_soft/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /chem_soft/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /chem_soft/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Looking whether force field files exist
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.rtp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.n2t
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.n2t
There are 23 name to type translations
Generating bonds from distances...
atom 0
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