Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread Mark Abraham
Hi, THR is parameterized for being part of a protein, yes. Mark On Mon, 30 Oct 2017 17:42 rose rahmani wrote: > i think ive got it now, you mean standalone aminoacids are inappropriate > for now,BUT they are usable in concept of proteins(as its particle),am i > right? > > On Mon, Oct 30, 2017

Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread rose rahmani
i think ive got it now, you mean standalone aminoacids are inappropriate for now,BUT they are usable in concept of proteins(as its particle),am i right? On Mon, Oct 30, 2017 at 7:38 PM, Mark Abraham wrote: > Hi, > > As I think Justin said a few days ago, force fields are typically > parameterize

Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread Mark Abraham
Hi, As I think Justin said a few days ago, force fields are typically parameterized for proteins, so THR means the dipeptide moiety, not e.g. the zwitterionic one. The latter would need many of the atoms to have different charges. It's essentially a different molecule, and one which the force fiel

Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread rose rahmani
yes of course On Mon, Oct 30, 2017 at 7:27 PM, R C Dash wrote: > can you please upload your PDB file? > > On Mon, Oct 30, 2017 at 11:41 AM, rose rahmani > wrote: > > > if it is included,so why AMBER doesnt identify amino acids like THR? > > error is such 'X' residuetype is not found in residue

Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread R C Dash
can you please upload your PDB file? On Mon, Oct 30, 2017 at 11:41 AM, rose rahmani wrote: > if it is included,so why AMBER doesnt identify amino acids like THR? > error is such 'X' residuetype is not found in residue topology > database? > i dont know what is the problem? > > thanks for you

Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread rose rahmani
if it is included,so why AMBER doesnt identify amino acids like THR? error is such 'X' residuetype is not found in residue topology database? i dont know what is the problem? thanks for your attention On Mon, Oct 30, 2017 at 6:25 PM, R C Dash wrote: > use https://atb.uq.edu.au/index.py / >

Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread R C Dash
use https://atb.uq.edu.au/index.py / http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg / or http://swissparam.ch/ or http://vienna-ptm.univie.ac.at/ for .itp file All amino acids are identified bybby AMBER force field. If you there is some modification like methylated lysine you have to creat a lib

Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread Vytautas Rakeviius
Generally you do not need such thing as parameters for amino acids come from force filed itself together with Gromacs.It you still want to make one just check scientific papers how force fields were created. On Monday, October 30, 2017, 4:41:50 PM GMT+2, rose rahmani wrote: hello h

Re: [gmx-users] itp file for aminoacids

2017-10-30 Thread Tasneem Kausar
You only need a pdb file for amino acids/proteins. pdb2gmx in gromacs does the job of making itp. Virus-free. www.avast.com

[gmx-users] itp file for aminoacids

2017-10-30 Thread rose rahmani
hello how can i make an .itp file for amino acids? which amino acids is identified in AMBER forcefield? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mai