[gmx-users] Using specbond.dat in pdb2gmx

Matthew Stancea mstancea at ggc.edu
Wed Jun 11 22:28:55 CEST 2014

? Hello,

I have been having a bit of issues generating an accurate gromacs topology file ("topol.top") utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost identical to the original pdb using the option "-ignh" at the end of my command, but doing so deletes the bond between the first nitrogen and the last carbon (which should be connected for this peptide to be cyclic) and adds two additional hydrogens and a positive charge to the first nitrogen and an additional oxygen and a negative charge to the last carbon, rendering this peptide as non-cyclic. After searching around for quite a while, I found out that many others on this mailing list were having the same issues as myself, and some replies to their messages including the usage of a file known as "specbond.dat" which may be helpful in retaining that bond.

However, I could not find an explanation of how to use this file in my command, and I was hoping someone could guide me on how to use specbond.dat in order to specify a particular bond. (I have tried both "-chainsep specbond.dat" and "-merge specbond.dat".)

I have been able to make a specbond.dat file that thoroughly explains what special bonds I need pdb2gmx to account for, but when I have tried to type a command file to use it, pdb2gmx generates topology files nearly identical to the topologies of the non-cyclic peptides when I had used the "-ignh" option rather than generating a cyclic peptide topol.top.

If more specific information is needed, I can provide that; however, I am not looking for an answer that is specific to my own issue, but rather a tutorial into generating a topology for gromacs from a pdb file of a cyclic peptide by using specbond.dat with pdb2gmx. (My version of pdb2gmx is 4.6.2.)

Thank you in advance.

-Matthew Stancea

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