On 10/22/12 8:46 PM, Nur Syafiqah Abdul Ghani wrote:
Dear All,
Right now i want to do another simulation which is water and co-solvent,HFIP.
I get the small compound file from
http://compbio.biosci.uq.edu.au/atb/download.py?molid=6187#files
I need to used the all atom one and the force field that i used is gromos96.
Right now i'm done packing the HFIP and the water by using packmol and
change all the pdb file into gro file.
Therefore I want to minimize them by using the command like below:
grompp -f em1.mdp -c mixture.gro -p topol.top -o minimize.tpr -v
and the error that coming out is :
Fatal error:
Syntax error - File solvent.itp, line 1
Last line read:
'[ atoms ]'
Invalid order for directive atoms
So, I already checked the problem by gedit the solvent.itp.Here is my itp file :
The first part of an .itp file needs to be a [moleculetype] directive that names
the molecule and defines its number of exclusions.
[ atoms ]
; nr type resnr resid atom cgnr charge mass total_charge
1 CH0 1 hfi C1 1 0.384 12.0110
2 F 1 hfi F1 1 -0.128 18.9984
3 F 1 hfi F2 1 -0.128 18.9984
4 F 1 hfi F3 1 -0.128 18.9984 ; 0.000
.............
9 CH0 1 hfi C3 3 0.384 12.0110
10 F 1 hfi F4 3 -0.128 18.9984
..........
; total charge of the molecule: 0.000
[ bonds ]
; ai aj funct c0 c1
1 2 2 0.1360 7.2300e+06
1 3 2 0.1360 4.7700e+06
...........
9 11 2 0.1360 4.7700e+06
9 12 2 0.1360 7.2300e+06
[ pairs ]
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp
1 8 1
1 10 1
1 11 1
1 12 1
2 6 1
.......
6 8 1
6 10 1
6 11 1
.......
7 11 1
7 12 1
8 9 1
[ angles ]
; ai aj ak funct angle fc
2 1 3 2 107.60 507.00
2 1 4 2 107.60 507.00
2 1 5 2 111.40 532.00
3 1 4 2 107.60 507.00
......
5 9 10 2 111.40 532.00
5 9 11 2 111.40 532.00
5 9 12 2 109.50 618.00
..........
11 9 12 2 107.60 507.00
[ dihedrals ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
[ dihedrals ]
; ai aj ak al funct ph0 cp mult
2 1 5 9 1 0.00 3.77 3
........
[ exclusions ]
; ai aj funct ; GROMOS 1-4 exclusions
and the topology file is :
The first thing you need to #include is the parent force field, from which
bonded and nonbonded parameters are taken.
-Justin
; Include topology for solvent
#include "solvent.itp"
;
; Include water topology
#include "gromos53a6.ff/spc.itp"
;
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
;
[ system ]
; Name
solvent in water box
;
;
[ molecules ]
; Compound #mols
hfi .......
Is thereany typing error that i seem cant see?
I already compare with other problem but seems that I'm lost.
Thanks in advance,
Best Regards,
Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
013-7188131
alternative email : [email protected]
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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