Re: Re: hexane

From: Jian Liu (
Date: Sun Oct 17 2010 - 23:10:34 CDT

Hi Dear Hasan

The line ‘’PATCHING FIRS NONE LAST NONE" is not necessary, but it is safe.

Mixing n-alkane is just like embeding proteins to a membrane or filling nanotubes with water,
you need to prepare individual pdb files each contains only ONE specie or ONE chain of prot/na.
In your case, you can do as following
1) separate the mixture.pdb to, f.e. pen.pdb and oct.pdb
2) the psfgen syntax:
psfgen> topology pentane.tpgpsfgen> topology octane.tpg ! or combine the two top file to a single one

psfgen> segment PEN { pdb pen.pdb }
psfgen> segment OCT { pdb oct.pdb }

psfgen> coordpdb pen.pdb PEN
psfgen> coordpdb oct.pdb OCT

psfgen> writepsf mix.psfpsfgen> writepdb mix.pdb
I am not sure weather packmol can generate the readable pdb file for psfgen.
The following is a well prepared pdb file.
If your pdb file is not similar with it, esp. the third column (C1, H11...),
you need to change them by hand (e.g. awk)
pdb> ATOM      1  C1  OCT A   1      -3.995   2.410  -0.000  1.00  0.00   
pdb> ATOM      2  H11 OCT A   1      -3.638   2.915   0.873  1.00  0.00   
pdb> ATOM      3  H12 OCT A   1      -3.638   2.915  -0.873  1.00  0.00   
pdb> ATOM      4  H13 OCT A   1      -5.065   2.410  -0.000  1.00  0.00   

May this can help you
Jian Liu

Master-degree Graduate Candidate Majoring in Molecular Modelling

----- Original Message -----
From: Hasan haska <>
To: Jian Liu <>
Subject: Re: namd-l: hexane
Date: 2010-10-17 22:52:19

Dear Jian Liu,
First of all, I new to NAMD and thank you very much for the octane top file you sent. Because I'm planning to perform binary n-alkane mixtures simulations using NAMD. So this top file will be very useful for me. But what does ‘’PATCHING FIRS NONE LAST NONE’ mean in top file ? Is it necessary to write it ?.
And I have some questions about generating a binary mixtures in NAMD. I planned a procedure, but I didn’t try if it works. The procedure is that: I want to use a packmol generated pdb file that includes for example 100 pentane and 50 octane. After I write seperately my top and parm files in Charmm file format for each alkane molecule I want to use psfgen to get a new pdb and psf file then I use these file with a conf file for the simulation. Is it true ? or do you have an alternative procedure or way to perform binary n-alkane mixtures simulations via NAMD ? I searched for a NAMD mixture simulation, but couldn’t get any info about it. Could you please explain your thoughts about this issue ? And If you have a conf file
 that you used for alkanes Could you please send it to me ?
Thank you very much for your help.
Best regards.
mix.pgn :
topology pentane.tpg
segment PEN {
 pdb mixture.pdb ! packmol file
topology octane.tpg
segment OCT {
 pdb mixture.pdb
coordpdb mixture.pdb
writepsf mix.psf
writepdb mix.pdb
In conf file: I use the files below
octane. prm

From: Jian Liu <>
To: lara lara <>; namd-l <>
Sent: Sun, October 17, 2010 4:32:09 AM
Subject: Re: namd-l: hexane

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

* >>> 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


RESI OCT 0.000
 C1 CT3 -0.27
ATOM H11 HA 0.09
ATOM H12 HA 0.09
ATOM H13 HA 0.09
ATOM C2 CT2 -0.18
ATOM H21 HA 0.09
ATOM H22 HA 0.09
ATOM C3 CT2 -0.18
ATOM H31 HA 0.09
ATOM H32 HA 0.09
ATOM C4 CT2 -0.18
ATOM H41 HA 0.09
ATOM H42 HA 0.09
ATOM C5 CT2 -0.18
ATOM H51 HA 0.09
ATOM H52 HA 0.09
ATOM C6 CT2 -0.18
ATOM H61 HA 0.09
ATOM H62 HA 0.09
ATOM C7 CT2 -0.18
ATOM H71 HA 0.09
ATOM H72 HA 0.09
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
 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 H81 C8 H82 C8 H83

May this can help you
Jian Liu
Master-degree Graduate Candidate Majoring in Molecular Modelling

---- Original Message ----
From: lara lara <>
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 .



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