[gmx-users] New residue in FF does not bond to others.

[Dawid das]

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