[gmx-users] CHARMM36 Termini Topology Incomplete

[Jarrett Lee Wise]

I had similar problems when I was making polymers.  You have to input those parameters directly or delete those lines in the itp/topology file depending if they are important or not.  The correct way would be to do quantum calculations for the missing parameters, but I inserted similar ones for the missing ones e.g. CH2 parameter for a CH1 parameter.


Jarrett Wise

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of João Rodrigues
Sent: Monday, May 04, 2015 1:44 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] CHARMM36 Termini Topology Incomplete

Hi all,

I am trying to setup a simulation of a peptide with neutral termini, using the CHARMM36 port from the MacKerell lab. While pdb2gmx works well, grompp fails with several erros about missing parameters, e.g.:

ERROR 1 [file topol.top, line 1225]:
  No default U-B types

...

ERROR 4 [file topol.top, line 1689]:
  No default Proper Dih. types

All these are related to the termini, whether I use CT2 or COOH, or NH2.
Could I copy the missing parameters from the old CHARMM27.ff files? Or should I contact the developers directly? The default charged termini work fine.

Or should I add the ACE/NMA caps in f.e. Pymol?

Cheers,

João
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