Re: hexane

From: lara lara (lara.4884_at_gmail.com)
Date: Sun Oct 17 2010 - 23:29:53 CDT

Dear Namd Users !

Thanks for the reply , Now I can understand the
topology file , but the file given for octane here
doesnot have the (IC ) values for exambel it is in the top_all22_prot.inp
for HSE as follows

IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991
IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166
IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446
IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290
IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505
IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578
IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833
IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109
IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114
IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101
IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859
IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596
IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170
IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782
IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929
IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996

my doubt is how one can define this for the same problem !

Is it possible to use the Hexane or Octane as the solvent as though one uses
the
TIP3P water for the simulation , if so how to do it ?

thanks in advance

lara

2010/10/17 Jian Liu <bay__gulf618_at_sina.com>

> 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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