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?
But how can I add the capping groups to the structure? > > > On 7/12/12 4:37 AM, [email protected] wrote: >> I have another question about the option -ter of the pdb2gmx command. >> >> I choose it because I thought that this is a way that I can determine >> what >> shell happen with the termini but I was not ask anything by the program. >> >> My aim is it to block the termini with a neutral group. Is there a way >> to >> do this with gromacs? >> > > Yes. You need to build the appropriate groups onto your protein's > structure > using normal capping groups present within the force field (ACE, NME, NH2, > etc) > and choose "None" for the termini when running pdb2gmx so that no > additional > protons are added or removed; the first and last amino acids are then > treated as > internal residues with normal peptide bonds. > > -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
