[AMBER] Forcefield_PTM

From: Sourav Purohit <sour000.gmail.com>
Date: Tue, 21 Oct 2014 17:55:40 +0530

Hi all.
The forcefield_PTM paper says that it is compatible with ff03. I tried to
use it with ff10 just to check what happens. While preparing the system in
xleap, it works fine. There is only one unusual warning about improper
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.

*Building improper torsion parameters.old PREP-specified impropers: <ALY
16>: CA H N -M <ALY 16>: CH CE NZ HZ <ALY 16>: CH3
NZ CH OH <ALY 16>: CA O C +M total 74 improper torsions
applied 4 improper torsions in old prep form*
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

    res total affected

    CASN 1
    NSER 1
    WAT 10351

What does this warning mean?? If I carry the simulation ahead with the
topology file generated, will the simulation be fine??

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Received on Tue Oct 21 2014 - 05:30:02 PDT
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