Dear Gromacs experts, I have found out why my force field does not work properly. I have added a new residue according to manual I found on Gromacs website. I modified all of the files. Now I have revealed that my new residue does not have connection to natural aminoacids in my topology file! If you take a look at it you will see that atoms 970 and 1009 are connected while the truth is that atoms 970 (carbonyl C atom of Phe65) and 1008 (MN1 atom of CH6 (new) residue) but also atoms 994 (MC3 atom of new residue) and 1009 (peptide N atom of Ser69) should be bonded. I have specified bonded parameters between those atom types in ffbonded.itp file but not in aminoacids.rtp. In other words my topology file does not recognize the connection between new residue and natural aminoacids residues. It seems like I do not specify something correctly in force field but I cannot find my mistake. Shall I specify this connection in specbond.dat file?
Best wishes, Dawid Grabarek PS Here you will find all relevant files (I guess and I hope so :) ) but if you need sth more, please give me a shout: http://www.speedyshare.com/Dk2tu/charmm27-files.tar.bz2 http://www.speedyshare.com/vtePQ/mCherry7.tar.bz2 -- 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.