Re: [AMBER] Solvating the system with polyethylene glycol PEG

From: Hector A. Baldoni <hbaldoni.unsl.edu.ar>
Date: Mon, 28 Jul 2014 15:08:00 -0300 (ARGSL-ST)

Hi,

Like this way:

source leaprc.ff99SB
source leaprc.gaff
loadamberprep cyh.prepin
mbox = copy CYH
solvatebox mbox CYH { 20.0 20.0 32.0 }
# solvatebox mbox MEOHBOX { 0.0 0.0 12.0 }
# solvatebox mbox TIP3PBOX { 0.0 0.0 35.0 }
SetBOX mbox vdw
saveamberparm mbox cyhbox.top cyhbox.crd
savePDB mbox cyhbox_leap.pdb
charge mbox
quit



Greeting,
Hector.



> Dear Amber users,
>
> I have develop library file for PEG molecule and want to solvate my
> simulation box using peg molecules rather than water. Could any one please
> guide how it could be done?
>
>
> thank you
> Iqbal
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


--------------------------------------
 Dr. Hector A. Baldoni
 Area de Quimica General e Inorganica
 Universidad Nacional de San Luis
 Chacabuco 917 (D5700BWS)
 San Luis - Argentina
 hbaldoni at unsl dot edu dot ar
 Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------


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Received on Mon Jul 28 2014 - 11:30:03 PDT
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