[gmx-users] Using specbond.dat in pdb2gmx

Matthew Stancea mstancea at ggc.edu
Wed Jun 18 23:09:07 CEST 2014

>>>> After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon.

>>> You need to be using -ter and choosing "None" for both termini, otherwise the
 default behavior takes over and pdb2gmx builds ionized termini.  You don't have
 free termini, so you have to take control of pdb2gmx.

>> I used the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter
 " and was asked about the protonation states for two of the residues, but I was not asked about the termini.

>Ah, because it's Amber.  Amber force fields are special and have specific
nomenclature that signifies N- and C-termini, so they automatically get built.
Changing the residue names by removing the N and C prefixes should fix things.

Okay, which file do I remove the N and C prefixes from?


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