Can you please give me an example of such a modeling software? I tried it with PYMOL but the results are not very good. And I also found several programs but the are all not free.
Thank you, Eva > > > On 7/12/12 6:12 AM, [email protected] wrote: >> Hi Justin, >> so you mean that I first have to add the capping groups to my structure >> and then run pdb2gmx with the -ter function? >> > > Yes. The capping groups (see your force field's .rtp file for available > entries) are treated as any other residue. Gromacs will not magically > build > them; they need to be present. > >> But how can I add the capping groups to the structure? >>> > > You'll have to use some external modeling software for that. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
