Re: [AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation

From: Jason Swails <>
Date: Wed, 9 Jun 2010 11:46:54 -0400


This file does not exist. It is the basis for the ff99SB force field
modifications as I understand it. You have a couple options. If you're
using tleap from AmberTools-1.4, a new constant pH leaprc file has been
created to automate all of these commands. Thus, all you have to do is
enter the command

source leaprc.constph

This will load constant pH parameters. This will, by default, load the
constant pH library with GL4 and AS4, as well as the frcmod.constph, and
change the default pbradii to mbondi2, as needed for constant pH

This file executes the following commands in your leap session:

source leaprc.ff99SB
loadamberparams frcmod.constph
loadoff constph.lib
set default pbradii mbondi2

If you don't use the leaprc.constph, then execute the above commands. The
instructions for starting constant pH simulations has been updated to use
leaprc.constph in the Amber11 manual, but it's still available for Amber10
through AmberTools 1.4.

Hope this helps,

On Wed, Jun 9, 2010 at 11:13 AM, Sangita Kachhap <>wrote:

> Hello all
> I have to do constant pH MD simulation using amber10 for this there is
> requirement of a file:
> frcmod.mod_phipsi.1
> But in amber10 there is no such any file.
> >From where i can get this file?
> There are option for editing PDB file for (HIS, HID, or HIE) with HIP,
> ASP and ASH to AS4 and all GLU and GLH to GL4, but there are no any option
> to
> change for
> LYS and TYR before preparation of prmtop and prmcrd file for constant pH
> MD
> simulation.
> Is there no need to change them or there are some other option?
> With regard
> Sangita Kachhap
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Wed Jun 09 2010 - 09:00:05 PDT
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