On 9/6/12 3:51 PM, Ali Alizadeh wrote:
Dear Justin
Thank you for your reply.
But i knew that,
i have a .itp file for example: heptane.itp:
[ moleculetype ]
; Name nrexcl
HEP 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 CH3 1 LIG CH31 1 0.0
2 CH2 1 LIG CH22 2 0.0
3 CH2 1 LIG CH23 3 0.0
4 CH2 1 LIG CH24 4 0.0
5 CH2 1 LIG CH25 5 0.0
6 CH2 1 LIG CH26 6 0.0
7 CH3 1 LIG CH37 7 0.0
[ bonds ]
; i j
1 2
2 3
3 4
4 5
5 6
6 7
[ angles ]
; i j k
1 2 3
2 3 4
3 4 5
4 5 6
5 6 7
[ dihedrals ]
; i j k l type
1 2 3 4 3
2 3 4 5 3
3 4 5 6 3
4 5 6 7 3
and my pdb file for heptane:
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.0
ATOM 1 C LIG 1 -5.231 0.634 -0.427 1.00 0.00 C
ATOM 2 H LIG 1 -5.407 -0.100 -1.242 1.00 0.00 H
ATOM 3 H LIG 1 -5.768 1.574 -0.673 1.00 0.00 H
ATOM 4 H LIG 1 -5.641 0.230 0.523 1.00 0.00 H
ATOM 5 C LIG 1 -3.739 0.920 -0.284 1.00 0.00 C
ATOM 6 H LIG 1 -3.595 1.672 0.522 1.00 0.00 H
ATOM 7 H LIG 1 -3.377 1.346 -1.242 1.00 0.00 H
ATOM 8 C LIG 1 -2.963 -0.360 0.064 1.00 0.00 C
ATOM 9 H LIG 1 -3.379 -0.775 1.009 1.00 0.00 H
ATOM 10 H LIG 1 -3.101 -1.119 -0.737 1.00 0.00 H
ATOM 11 C LIG 1 -0.728 0.352 -0.983 1.00 0.00 C
ATOM 12 H LIG 1 -0.896 -0.406 -1.780 1.00 0.00 H
ATOM 13 H LIG 1 -1.130 1.324 -1.336 1.00 0.00 H
ATOM 14 C LIG 1 0.790 0.492 -0.786 1.00 0.00 C
ATOM 15 H LIG 1 1.220 -0.478 -0.454 1.00 0.00 H
ATOM 16 H LIG 1 1.242 0.752 -1.768 1.00 0.00 H
ATOM 17 C LIG 1 -1.461 -0.115 0.288 1.00 0.00 C
ATOM 18 H LIG 1 -1.340 0.624 1.106 1.00 0.00 H
ATOM 19 H LIG 1 -1.009 -1.077 0.616 1.00 0.00 H
ATOM 20 C LIG 1 1.172 1.589 0.209 1.00 0.00 C
ATOM 21 H LIG 1 0.797 1.360 1.226 1.00 0.00 H
ATOM 22 H LIG 1 0.764 2.568 -0.123 1.00 0.00 H
ATOM 23 H LIG 1 2.278 1.667 0.264 1.00 0.00 H
Above file is only for one molecule.
How to i use this pdb file for the .itp file ?(If i have 1000 heptane molecules)
Can I use VMD software?
I don't know if VMD can do that. You can easily remove the H atoms with a
simple grep command (grep -v H heptane.pdb > heptane_noH.pdb). Then you need to
rename the atoms as the topology expects. Building a box of 1000 heptane
molecules can be done with Gromacs tools using this "clean" coordinate file.
See http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation.
-Justin
--
========================================
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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