vinothkumar mohanakrishnan wrote:
hi i have 20 coordinates in the .gro file from PRODRG server where as i
have only 6 atom coordidates in the .top file this file also i got from
PRODRG. below i am giving both my .top file as well as .gro file for
hexane. do i manually edit the .top file from PRODRG to match the
coordinates, if so how?.my worry again is when i give this command
You're trying to use an all-atom coordinate file with a united-atom force field.
Do not try to add atoms to the topology. Use an appropriate coordinate file.
Also, the charges assigned to the hexane molecule (like much of the output from
PRODRG) are probably not correct. In UA force fields like Gromos, aliphatic
groups should be uncharged. Note that there is a charge imbalance in your
molecule, such that there is a permanent, albeit small, net dipole on the
molecule. Ask yourself: does this model reflect reality?
genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o
hexane_multi.gro -nmol 100 -seed 1997
the .top file doesn't get updated with more number (say 101) of hexane
molecules in the molecules section.kindly advice me on this point.
Perhaps the box you're using simply can't fit more than 101 molecules.
-Justin
hexane.top
#include "ffG43a1.itp"
[ moleculetype ]
; Name nrexcl
hexane 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CAA 1 -0.018 15.0350
2 CH2 1 DRG CAB 1 0.011 14.0270
3 CH2 1 DRG CAC 1 0.008 14.0270
4 CH2 1 DRG CAD 1 0.009 14.0270
5 CH2 1 DRG CAE 1 0.009 14.0270
6 CH3 1 DRG CAF 1 -0.019 15.0350
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAA
2 3 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAC
3 4 2 0.153 7150000.0 0.153 7150000.0 ; CAC CAD
4 5 2 0.153 7150000.0 0.153 7150000.0 ; CAD CAE
5 6 2 0.153 7150000.0 0.153 7150000.0 ; CAE CAF
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; CAA CAD
2 5 1 ; CAB CAE
3 6 1 ; CAC CAF
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 109.5 520.0 109.5 520.0 ; CAA CAB
CAC
2 3 4 2 109.5 520.0 109.5 520.0 ; CAB CAC
CAD
3 4 5 2 109.5 520.0 109.5 520.0 ; CAC CAD
CAE
4 5 6 2 109.5 520.0 109.5 520.0 ; CAD CAE
CAF
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD
CAC CAB CAA
5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAE
CAD CAC CAB
6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF
CAE CAD CAC
; Include SPC water topology
#include "spc.itp"
[ system ]
hexane in water
[ molecules ]
;molecule name number
hexane 101
SOL 1764
hexane.gro
PRODRG COORDS
20
1DRG CAA 1 0.684 -0.063 1.332
1DRG HAA 2 0.684 0.013 1.254
1DRG HAB 3 0.583 -0.075 1.371
1DRG HAC 4 0.724 -0.158 1.295
1DRG CAB 5 0.778 -0.021 1.445
1DRG HAD 6 0.776 -0.098 1.522
1DRG HAE 7 0.744 0.077 1.479
1DRG CAC 8 0.923 -0.003 1.396
1DRG HAF 9 0.950 -0.087 1.332
1DRG HAG 10 0.985 0.007 1.485
1DRG CAD 11 0.940 0.127 1.316
1DRG HAH 12 0.913 0.211 1.380
1DRG HAI 13 0.878 0.117 1.227
1DRG CAE 14 1.085 0.145 1.267
1DRG HAJ 15 1.087 0.222 1.190
1DRG HAK 16 1.118 0.047 1.232
1DRG CAF 17 1.179 0.186 1.380
1DRG HAM 18 1.149 0.284 1.418
1DRG HAN 19 1.281 0.191 1.342
1DRG HAL 20 1.168 0.108 1.456
0.84818 0.84818 0.84818
Regards
Vinoth
On Mon, Sep 13, 2010 at 4:26 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
vinothkumar mohanakrishnan wrote:
i want to do MD for hexane-water system. I got hexane.gro and
hexane..itp from PRODRG 2.5 Beta server with that i made the
hexane.top file. below is the serious of commands i executed in
gromacs, i am adding 200 hexane molecules an 1115 water
molecules. after the first genbox i checked my topolgy file
wheather the no .of hexane molecules got updated r increased to
200 but it doesn't and remains as 1 and then i maually changed
it to 200 in the molecules section. i dont know where
Per your genbox command below, if you have one hexane (in
hexane_box.gro) and you add 200 (with -nmol), you should then have
201 hexane molecules in the system.
iam going wrong and i always get the error message as " number
of coordinates in coordinate file (hexane_solv.gro, 7365) does
not match topology (hexane.top, 4545) " while running grompp for
energy minimisation. i read the error gromacs (website)
documentation and found that the hexane.top r hexane.gro file is
not getting updated, but iam helpless. any help is highly
appreciated. below is my topology file as well.
Follow my previous advice and see if you can trace back where the
error came from. Count the molecules in your .gro file, i.e.:
grep OW hexane_solv.gro | wc -l
will give you the number of water molecules. Do something analogous
for hexane. You're off by 2820 atoms, which is in the ballpark of
940 waters, so something has broken down pretty badly somewhere.
-Justin
; The force field files to be included
#include "ffG43a1.itp"
; Include hexane topology
#include "hexane.itp"
; Include SPC water topology
#include "spc.itp"
[ system ]
hexane in Water
[ molecules ]
;molecule name number
hexane 200
SOL 1115
*
Commands*
editconf -f hexane.gro -o hexane_box.gro -c -bt triclinic -box
8.31 3.01 3.01
genbox -cp hexane_box.gro -ci hexane_box.gro -p hexane.top -o
hexane_multi.gro -nmol 200 -seed 1997
genbox -cp hexane_multi.gro -cs spc216.gro -p hexane.top -o
hexane_solv.gro
grompp -f em.mdp -c hexane_solv.gro -p hexane.top -o hexane_em.tpr
Regards
Vinoth
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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========================================
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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