On 5/12/15 12:36 AM, Andrew Bostick wrote:
Dear Justin Very thanks for your answer I should use my pdb file in which there is no bond between CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from peptide 2. Creating new entry in specbond.dat file will consider this new bond. Is my vision true? Based on your answer, only thing I should do is creating a new entry in specbond.dat? Should I don't other thing?
As I said, you need a new entry in specbond.dat and special .rtp entries.
Based on following link ( http://www.gromacs.org/Documentation/File_Formats/specbond.dat), my new entry is as follows, is it true? GLU CD 1 LYS NZ 1 0.13 GLU2 LYS2 How to get the accurate reference length for searching for candidate bonds?
Well, what should be the C-N bond length in a normal peptide bond?
In my system there is more than 1 Lys and 1 Glu residues. I want this new bond between special residue of Lys (for example number: 28 ) and special residue of Glu (for example number: 45). How to set this state in specbond.dat file?
This is what the distance column is for; special linkages are only created if the distance between the specified atoms is within 10% of that criterion.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
