[gmx-users] berger lipid parameters in amber99sb-ildn ff

Monoj Mon Kalita mon.123chem at gmail.com
Tue Mar 25 02:57:14 CET 2014

Dear Chris

Sorry, That didn't solve my problem. I tried that option ,before posting
here, with different authors from two publications, but seems no reply from
anybody. I wish, I could find somebody in this mailing list who is willing
to put forward his/her advice or share their experience with me to solve
this issue. Many thanks in advance.

Message: 1
Date: Sun, 23 Mar 2014 11:32:44 +0000
From: Christopher Neale <chris.neale at alum.utoronto.ca>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] berger lipid parameters in amber99sb-ildn ff
91dc2bfb46004e1b9fa1a8922bb55ae6 at BLUPR03MB184.namprd03.prod.outlook.com>

Content-Type: text/plain; charset="us-ascii"

See this paper for Amber protein and berger lipids:


If you contact the authors, I am sure that they can send you the files.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Monoj Mon
Kalita <mon.123chem at gmail.com>
Sent: 23 March 2014 00:29
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] berger lipid parameters in amber99sb-ildn ff

Dear Users

I am trying to run a drug-protein simulation in GROMACS. I have calculated
the ligand paramteres using the generalized amber force field (GAFF) . ESP
partial charges were calculated using HF/6-31G* basis set. RESP fitting was
performed using the Antechamber . Now I am having trouble in introducing
the berger lipid parameters into the topology file created by
amber99sb-ildn ff . All I got are gromos adopted forcefield files and
berger lipid parameters as I want to run my simulation in united-atom POPC
membrane with berger lipid parameter and amber99sb-ildn ff for protein. Is
there any link to download the amber adopted toplogy file for united atom
POPC with berger lipid forcefield parameters which may solve my problem.

I am following the method mentioned in this publication doi:
10.3109/09687688.2013.773095. to set up my protocol.


 With Regards
Monoj Mon Kalita
Taipei, Taiwan


With Regards

Monoj Mon Kalita
Taipei, Taiwan

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