Itamar, thank you for advise but I dont like swith prot :)) Justin, what xleap prameter set have you used for KALP peptide? I want to find parameters wich would not affect any problems in my further simulation via gromos in Gromacs.
James 2011/10/31 Itamar Kass <itamar.k...@monash.edu> > Hi James, > > I usually use Swiss-PdbViewer (http://spdbv.vital-it.ch/disclaim.html). > Despite being an old and not well supported for any system, it is still a > free and easy to use and allows the building and mutating of residues in > addition to automatically adding missing atoms. > > You can just build an extra GLY at the end of the your chain and using > text editor change it to N/C-caps. > > > Cheers, > Itamar > > On 31/10/2011, at 11:16 PM, Dr. Vitaly V. Chaban wrote: > > Dear Gromacs Users! > > > > I'd like to know about external software wich could be used for structure > > processing for the futher simulation in Gromacs. Today I've tried one of > the > > most popular such software Amber tools but I've forced with problems during > > compilation of it ") So I'm looking for possible analogues ) > > > First of all I'm intresting in software for the addition different CAPing > > groups to N and C termi of my protein. > > > Is there any plugins for Pymol or VMD for such purposes? I've loked for > this > > option in both of that software but couldnot find > > > > Thank you for your help, > > > James > > > Among free solutions... maybe this would help: > http://www.chemaxon.com/marvin/sketch/index.php > > I don't know molecular editor plugins for VMD, but it would be cool, > if one is accessible. > > -- > Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. > Univ. Rochester, Rochester, New York 14627-0216 > THE UNITED STATES OF AMERICA > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > > "In theory, there is no difference between theory and practice. But, in > practice, there is." - Jan L.A. van de Snepscheut > > =========================================== > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: itamar.k...@monash.edu > ============================================ > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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