Re: hexane

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



This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:18 CST