Hi,
With my grompp.mdp,topol.top and gonf.gro i gave the command and the output
was
[abhi...@scfbioserver gromacs]$ grompp -f grompp.mdp -p topol.top -c
conf.gro -o water.tpr
:-) G R O M A C S (-:
Gravel Rubs Often Many Awfully Cauterized Sores
:-) VERSION 4.0.4 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
Option Filename Type Description
------------------------------------------------------------
-f grompp.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c conf.gro Input Structure file: gro g96 pdb tpr tpb tpa
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p topol.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o water.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input
processing
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'cpp'
checking input for internal consistency...
NOTE 1 [file grompp.mdp, line unknown]:
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
processing topology...
-------------------------------------------------------
Program grompp, VERSION 4.0.4
Source code file: topio.c, line: 415
Fatal error:
Syntax error - File topol.top, line 4
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
-------------------------------------------------------
"I believe in miracles cause I'm one" (The Ramones)
[abhi...@scfbioserver gromacs]$
my topol.top file is
xirs fudgeLJ fudgeQQ
1 2 yes 0.5 0.5
[ atomtypes ]
;name at.num mass charge ptype sigma epsilon
OW 8 15.99940 0.000 A 0.3166 0.65
HW 1 1.00800 0.000 A 0.00000E+00 0.00000E+00
;---------------------------------------------------------------
; Definition of the SPC/E water model---------------------------
;
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 SOL OW 1 -0.8476
2 HW 1 SOL HW1 1 0.4238
3 HW 1 SOL HW2 1 0.4238
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330
[ exclusions ]
1 2 3
2 1 3
3 1 2
;---------------------------------------------------------------
; End of definition of the SPC/E water model--------------------
;---------------------------------------------------------------
[ system ]
Water SPC/E
[ molecules ]
SOL 216
the conf.gro file is
203SOL HW1 608 1.821 0.322 0.817 0.8928 1.1548 0.7389
203SOL HW2 609 1.875 0.440 0.718 -1.9604 0.3767 -1.7905
204SOL OW 610 0.779 1.345 0.916 0.2112 -0.0070 0.2315
204SOL HW1 611 0.686 1.338 0.954 0.8109 -1.6887 1.4414
204SOL HW2 612 0.805 1.442 0.909 -2.0435 0.5275 -1.1795
205SOL OW 613 1.718 1.114 0.507 0.2154 -0.1127 -0.1792
205SOL HW1 614 1.755 1.098 0.416 -0.9406 -0.2600 -0.6191
205SOL HW2 615 1.769 1.060 0.574 -1.8561 -3.6296 -1.3196
206SOL OW 616 0.694 0.641 1.677 0.0172 0.0058 -0.2012
206SOL HW1 617 0.784 0.654 1.717 1.2820 -2.2353 -2.2392
206SOL HW2 618 0.647 0.566 1.723 -1.1125 1.6018 1.2995
207SOL OW 619 1.089 0.525 0.672 0.1215 -0.1196 -0.1599
207SOL HW1 620 1.124 0.538 0.579 0.9751 2.2078 0.4622
207SOL HW2 621 0.995 0.490 0.668 -1.9486 5.2441 -2.0093
208SOL OW 622 1.644 0.521 0.536 0.8695 -0.0305 0.4538
208SOL HW1 623 1.568 0.521 0.602 1.0461 -0.1378 0.6487
208SOL HW2 624 1.683 0.429 0.530 0.6027 -0.1103 -0.0867
209SOL OW 625 1.607 0.804 1.136 0.1924 -0.0775 -0.0451
209SOL HW1 626 1.700 0.841 1.138 -0.3765 1.4071 -1.2113
209SOL HW2 627 1.602 0.725 1.198 1.8134 0.8052 1.2429
210SOL OW 628 0.961 1.176 0.727 0.0667 0.1065 0.0824
210SOL HW1 629 0.878 1.218 0.765 0.0936 -0.8745 1.2584
210SOL HW2 630 0.959 1.078 0.744 0.3982 -0.2571 -1.9273
211SOL OW 631 1.441 1.835 1.811 0.4461 -0.3668 -0.0023
211SOL HW1 632 1.478 1.796 1.727 -1.1085 -1.3547 -0.2480
211SOL HW2 633 1.442 1.766 1.884 -1.2578 -0.5603 -0.1372
212SOL OW 634 0.594 0.650 0.961 0.1032 0.4852 0.5329
212SOL HW1 635 0.642 0.644 1.049 0.6450 -0.1007 0.1907
212SOL HW2 636 0.660 0.659 0.887 -0.3688 1.3618 0.2061
213SOL OW 637 1.227 1.503 0.161 -0.0292 -0.8161 0.3425
213SOL HW1 638 1.225 1.458 0.251 0.3570 -0.7808 0.3667
213SOL HW2 639 1.136 1.535 0.138 -0.2322 -1.2929 0.4912
214SOL OW 640 0.606 0.647 1.408 -0.1516 -0.3989 0.3259
214SOL HW1 641 0.639 0.672 1.499 -1.3540 1.1041 0.3654
214SOL HW2 642 0.591 0.548 1.404 2.9386 -0.9536 0.7368
215SOL OW 643 1.607 1.679 0.596 0.1020 -0.0876 0.2788
215SOL HW1 644 1.558 1.743 0.537 -1.2519 -2.7009 -1.5800
215SOL HW2 645 1.542 1.635 0.658 0.9367 0.0657 1.2497
216SOL OW 646 1.663 1.409 0.500 0.3668 0.1318 0.2586
216SOL HW1 647 1.652 1.490 0.558 0.1481 1.3472 -1.4439
216SOL HW2 648 1.644 1.327 0.554 0.0397 1.2345 1.8708
1.85058 1.85058 1.85058
and thegrompp.mdpo file is
tc-grps = System
tau_t = 0.1
ref_t = 300
Pcoupl = No
gen_vel = yes
gen_temp = 300
gen_seed = 1993
PCE model
cpp = /usr/bin/cpp
include =
define =
integrator = md
dt = 0.001
nsteps = 50000
nstxtcout = 100
xtc-precision = 1000
rlist = 0.9
coulombtype = Cut-off
rcoulomb = 0.9
vdw-type = Cut-off
rvdw = 0.9
DispCorr = EnerPres
Tcoupl = berendsen
tc-grps = System
tau_t = 0.1
ref_t = 300
Pcoupl = No
gen_vel = yes
gen_temp = 300
gen_seed = 1993:x
so what is the problem
Abhijit Kayal
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