First, calculate the number of Na+ and Cl- ions you need to add.
Then, use these commands in leap
Loadamberparams frcmod.ionsjc_tip3p
Addions <system> Na+ <num of ions>
Addions <system> Cl- <num of ions>
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: zeba firdows [mailto:zebafirdows197.gmail.com]
Sent: Friday, February 03, 2017 4:56 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] protocol for simulating a system in NaCl using xleaP module
Yes, like we add water to our system. In a similar way i want NaCl to be added or dissolved in my system.
*With Regards,Zeba Firdows*
*Dept. of MBBT*
*Tezpur University*
On Fri, Feb 3, 2017 at 3:21 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Do you mean that you want to add NaCl to your system?
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry) at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in
> Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: zeba firdows [mailto:zebafirdows197.gmail.com]
> Sent: Friday, February 03, 2017 12:57 PM
> To: amber.ambermd.org
> Subject: [AMBER] protocol for simulating a system in NaCl using xleaP
> module
>
> We usually prepare the systems in xleap using implicit solvation or
> explicit solvation but i want to know the method of how to prepare the
> system in presence of NaCl. Kindly provide me the protocol.
> Thanking you
>
> *With Regards,Zeba Firdows*
> *Dept. of MBBT*
> *Tezpur University*
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> AMBER mailing list
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>
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Received on Fri Feb 03 2017 - 04:00:02 PST
