[gmx-users] pdb2gmx and periodic molecule

Alex nedomacho at gmail.com
Sun Apr 26 05:34:36 CEST 2015


I am not entirely sure I understand your sequence of steps. Why do you
want to first run it normally, but then also without adding the
hydrogens? The hydrogens (a total of two) are only added at the
termini by default, and in the final product there's no
need for them anyway.

Here's what I'm able to understand: run as usual, delete all bonded data
relevant to termini, add bonded descriptions for the residues at the
boundary, modify pdb to remove termini (actually, I can generate the
periodic ones automatically). Am I missing something that
should make my life easier?

Also, is there a way to automate this by modifying the forcefield?
See, right now (on the periodic structure without termini) pdb2gmx
sees the first residue and looks it up as one with a terminus, which
is really the gist of the error it throws, so I doubt it even gets to
the point of looking at the boundary. Is it that the utility behavior
cannot be changed at the ff level, and thus our only
option is manual modification of the topology?

Thank you,


JL> pdb2gmx isn't designed to intuitively handle such cases.  The best way to go
JL> about it is:

JL> 1. Run pdb2gmx normally to add H that you might need and to apply patching such
JL> that you have a phosphate on one end and an alcohol on the other (presumably you
JL> already have this last part done and have suitable .tdb entries).

JL> 2. Delete unnecessary atoms from the termini.

JL> 3. Run pdb2gmx again with -ter (choose None) and -missing so that it doesn't
JL> complain at you about dangling termini.

JL> 4. Manually edit the topology to introduce the needed bond, angles, and dihedrals.

JL> -Justin

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