From: Jian Liu (bay__gulf618_at_sina.com)
Date: Sat Oct 16 2010 - 20:32:09 CDT
Ji Hear Lara
Here attached a top file I used for octane.
It would be easy to change it to hexane following some protocols.
The format of top file are appendixed in namd user's guide.
If you want to learn further more, you can have a look of:
1) Parameterizing a Novel Residue and
2) Topology File Tutorial
on http://www.ks.uiuc.edu/Training/Tutorials/
----------------
* >>> topology file for octane
0 1
MASS 3 HA 1.00800 H ! nonpolar H
MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2
MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3
AUTO ANGLES DIHE
RESI OCT 0.000
GROUP
ATOM C1 CT3 -0.27
ATOM H11 HA 0.09
ATOM H12 HA 0.09
ATOM H13 HA 0.09
GROUP
ATOM C2 CT2 -0.18
ATOM H21 HA 0.09
ATOM H22 HA 0.09
GROUP
ATOM C3 CT2 -0.18
ATOM H31 HA 0.09
ATOM H32 HA 0.09
GROUP
ATOM C4 CT2 -0.18
ATOM H41 HA 0.09
ATOM H42 HA 0.09
GROUP
ATOM C5 CT2 -0.18
ATOM H51 HA 0.09
ATOM H52 HA 0.09
GROUP
ATOM C6 CT2 -0.18
ATOM H61 HA 0.09
ATOM H62 HA 0.09
GROUP
ATOM C7 CT2 -0.18
ATOM H71 HA 0.09
ATOM H72 HA 0.09
GROUP
ATOM C8 CT2 -0.27
ATOM H81 HA 0.09
ATOM H82 HA 0.09
ATOM H83 HA 0.09
BOND C1 H11 C1 H12 C1 H13
BOND C2 C1 C2 H21 C2 H22
BOND C3 C2 C3 H31 C3 H32
BOND C4 C3 C4 H41 C4 H42
BOND C5 C4 C5 H51 C5 H52
BOND C6 C5 C6 H61 C6 H62
BOND C7 C6 C7 H71 C7 H72
BOND C8 C7
BOND C8 H81 C8 H82 C8 H83
PATCHING FIRS NONE LAST NONE
END
-------------------
May this can help you
------------------------------------------------
Jian Liu
Master-degree Graduate Candidate Majoring in Molecular Modelling
http://is.gd/ducip
----- Original Message -----
From: lara lara <lara.4884_at_gmail.com>
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: hexane
Date: 2010-10-16 17:00:09
dear namd !
I have seen the topology file but I could not understand .
can any one tell me how to build the
topology for the hexane molecule .
regards
lara
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