Hi, I have a capped peptide (ACE-ALA-NME) and now when i add the other molecules through the command "gmx insert-molecules", the residue id of the capped peptide, which was 1 as: 1ACE CH3 1ACE HH31 1ACE HH32 1ACE HH33 1ACE C 1ACE O 1ALA N 1ALA HN 1ALA CA 1ALA HA 1ALA CB 1ALA HB1 1ALA HB2 1ALA HB3 1ALA C 1ALA O 1NME N 1NME HN 1NME CH3 1NME HH31 1NME HH32 1NME HH33 gets changed to 1,2 and 3 as in: 1ACE CH3 1ACE HH31 1ACE HH32 1ACE HH33 1ACE C 1ACE O 2ALA N 2ALA HN 2ALA CA 2ALA HA 2ALA CB 2ALA HB1 2ALA HB2 2ALA HB3 2ALA C 2ALA O 3NME N 3NME HN 3NME CH3 3NME HH31 3NME HH32 3NME HH33 4XYZ N1 4XYZ N2 4XYZ C1 and so on...
1] How can i prevent the residue id's from getting changed..??(or) retain their residue id's..? 2] Since when residue id's gets changed, it is treated as different chains/molecules and bonds between them are shown as "Warning) Unusual bond between residues: 1(none) and 2 (protein) Warning) Unusual bond between residues: 2 (protein) and 3 (none)" when viewed in VMD. causing a problem... Any suggestions are highly appreciated. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> 15/11/18, 11:02:34 -- 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.