Thank you very much Dr. Case for reaching out soon. This was a relief to hear. But now I have another doubt.
For the ligand discharging step I have to do TI simulations with start state and ending state. In sander I can group two prmtop for this purpose. If I'm using crgmask to remove charges, shouldn't both of my prmtop be the same?
Senal Dinuka
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Thursday, September 17, 2020 9:12:15 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Perturbing charges
On Thu, Sep 17, 2020, Delwakkada Liyanage, Senal Dinuka wrote:
>
>I'm trying to derive parameters for a TI state where the ligand is
>supposed to disappear from solvent. I have gone through both the TI
>tutorials A9 and older Amber9 tutorial for toluene disappearance. Given
>that I'm dealing with a fairly large ligand with 90 atoms, I like to
>know if there is any straightforward approach to change charges in xleap
>rather than one by one.
Check out the 'crgmask' paramter (Chap 23), which allows you to easily
set certain charges to zero.
>
>Also does a amber OFF file holds all the information in a prepi or frcmod file?
An OFF file has the same info as prepi. It does *not* contain force
field paramters that would be in a frcmod file.
....dac
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Received on Fri Sep 18 2020 - 06:00:04 PDT
