Hi Justin,
That makes sense, I've found where the parameters are
Thanks for your help
James
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: 14 February 2018 22:31:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-user
Hi Justin,
Many thanks for the detailed reply.
I just wanted to check that it doesn't matter that the A2C and A3C are not
present in the bonded and non-bonded itp files for the forcefield? Should this
not have given an error?
Kind regards,
James
From: gromacs.
Thanks Justin,
Will this effect the interactions (both bonded and non-bonded) that these atoms
have, as their atom types are not in the forcefield itp files?
Kind regards,
James
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Le
Hi,
I've used acpype to convert my prmtop and inpcrd files into gromacs format. I'm
using the amber14sb forcefield.
At the top of the top file generated, is an [atomtypes] section. Most of the
atoms in this section were present in the atomtypes.atp and ffnonbonded.itp so
I deleted them howev
Dear Maud,
Thanks, I will give that a try,
Regards,
James
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Maud Jusot
Sent: 17 October 2017 16:10:42
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Creating cyclic peptides
Dear Jame
Thanks Justin,
Is there anyway of getting it to work using an AMBER forcefield as well?
Kind regards,
James
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: 17 October 2017 15:46:27
To: gmx-us...@gromacs.org
Subject
Hi,
I'm trying to create a cyclic hexapeptide using pdb2gmx. I want to be able to
do this using either an AMBER or CHARMM forcefield.
Initially I have been following the instructions in this link,
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html
Howev
