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 <mark.j.abra...@gmail.com> wrote: > 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 > field designers might or might not have felt important to target. If you > need the standalone amino acids, then you should choose your force field > (plus perhaps topology+parameter generation strategy) with that in mind, > rather than assuming that any particular force field is appropriate, and > then trying to make your square problem fit in that round hole. > > Mark > > On Mon, Oct 30, 2017 at 5:04 PM rose rahmani <rose.rhm...@gmail.com> > wrote: > > > yes of course > > > > On Mon, Oct 30, 2017 at 7:27 PM, R C Dash <rcdash0...@gmail.com> wrote: > > > > > can you please upload your PDB file? > > > > > > On Mon, Oct 30, 2017 at 11:41 AM, rose rahmani <rose.rhm...@gmail.com> > > > 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 your attention > > > > > > > > On Mon, Oct 30, 2017 at 6:25 PM, R C Dash <rcdash0...@gmail.com> > > wrote: > > > > > > > > > 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 > file > > > and > > > > > use it in tleap AMBERTools. > > > > > > > > > > On Mon, Oct 30, 2017 at 10:48 AM, Tasneem Kausar < > > > > > tasneemkausa...@gmail.com> > > > > > wrote: > > > > > > > > > > > You only need a pdb file for amino acids/proteins. pdb2gmx in > > gromacs > > > > > does > > > > > > the job of making itp. > > > > > > > > > > > > <https://www.avast.com/sig-email?utm_medium=email&utm_ > > > > > > source=link&utm_campaign=sig-email&utm_content=webmail> > > > > > > Virus-free. > > > > > > www.avast.com > > > > > > <https://www.avast.com/sig-email?utm_medium=email&utm_ > > > > > > source=link&utm_campaign=sig-email&utm_content=webmail> > > > > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > > > > > > > > > > On Mon, Oct 30, 2017 at 8:11 PM, rose rahmani < > > rose.rhm...@gmail.com > > > > > > > > > > wrote: > > > > > > > > > > > > > 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? 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