Dear Users,
I had raised a ticket regarding this problem that I
faced dated back to march 7th, 2020. Unfortunately, I couldn't able to
solve the problem till now and also didn't get any suggestions from any
users. So, I am mailing again to grab the user's attention in this regard.
Please help.
Thanks in advance,
Satyajit
Message: 4
Date: Sat, 7 Mar 2020 12:44:32 +0530
From: SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
Subject: [AMBER] Unavailability of the file related to -cprestrt flag
in equilibration (NPT) step of constant pH MD in Amber14 with
AmberTools15
To: amber.ambermd.org
Message-ID:
<CAOoM83scVpX5C-hpBf==TneX4Rm5f4tesWe=97e4+bZCmdjqfw.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear Users,
I am doing a const pH MD simulations of an enzyme in
explicit solvent and I have followed this tutorial
http://jswails.wikidot.com/explicit-solvent-constant-ph-md for system
preparation as well as for inputs. And for running simulation followed the
tutorial provided in Amber advanced tutorials section
https://ambermd.org/tutorials/advanced/tutorial18/section2.htm. Up to
heating it seems that there was no problem as it generated all required
files without showing any kind of errors. But when I ran equilibration using
NPT ensemble, there was no file which supposed to be created by -cprestrt
flag. I have tried pmemd modules (both Cuda and Cuda.MPI) of AMBER for the
run, however, the problem persists. Can someone tell me what I have done
wrong here? Please help.
Thanks a lot,
Satyajit
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Received on Sat Sep 05 2020 - 00:30:02 PDT
