Would you please let me know if it is acceptable to add dihedrals and angles and bonds? and not to add any pairs to the top? just deleting the pairs which are added by pdb2gmx incorrectly to the terminus?
And I don't know that if I don't add all bonds or dihedrals what would happen? How would I be sure that I have added all modifications completely? Sincerely, Shima ________________________________ From: Justin Lemkul <[email protected]> To: Shima Arasteh <[email protected]> Sent: Tuesday, March 19, 2013 9:00 PM Subject: Re: [gmx-users] Top file modification On Tue, Mar 19, 2013 at 1:28 PM, Shima Arasteh <[email protected]> wrote: :) > > >In fact, I have a NMR pdb file of a cyclic peptide. To get a proper gro and >topology files, I ran pdb2gmx without -ter flag. Then tried to modify the top >file. Is there any better ideas? > > Manual modification in that case is probably reasonably safe, as long as you are careful to use parameters that are appropriate for all bonded and nonbonded interactions that change as a result of the modification. -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 * 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
