Thanks, Yang Ye. You mean that I put an additional ACE or NME on the N-terminal lysine residue?
zhongqiao > Message: 3 > Date: Fri, 09 Nov 2007 20:03:21 +0800 > From: Yang Ye <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] How to set N-terminal lysine carry only +1 > unit charge? > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > it could not be possible since amber force field doesn't parameterized > NLYN. alternative, use ACE/NME to cap the peptide. > > On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: > > > > Hi, > > > > > > > > I am using amber force field in Gromacs. The protein I simulated is > > the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be > > neutral. According to rules using Amber in Gromacs, neutral lysine > > should be named to LYN. Everything goes smoothly except the N-terminal > > lysine residue. It should carry +1 unit charge due to its location. > > According to the rules, I should rename this residue as NLYN. But I > > can not find NLYN in ffamber*.rtp. In other words, error will appear > > if I do so. I did not get response from Dear Dr. Eric J. Sorin who > > establish amber port into gromacs. So anyone knows how to set > > N-terminal lysine residue carry +1, not +2 unit charges using Amber FF > > in gmx? > > > > > > > > Zhongqiao > > > > > > > > National University of Singapore _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
