Re: [AMBER] Problem with penta coordinated HEME-HIS

From: Jason Swails <>
Date: Thu, 21 Nov 2013 07:52:03 -0500

On Thu, 2013-11-21 at 08:18 +0530, wrote:
> Hi Jason,
> Thanks a lot for your reply.
> I am using the following tleap script to add a bond between HEME and HIS.
> loadamberparams frcmod.hemall
> loadamberprep
> addAtomTypes { { "DZ" "Zn" "sp3" } { "Zn" "Zn" "sp3" } }
> loadOff znb.lib
> loadOff hin.lib
> loadOff hydroxide.lib
> loadamberparams frcmod.zinc
> fep = loadpdb clnFePPIX.pdb
> bond fep.103.13 fep.181.1
> addions fep Na+ 0
> solvatebox fep TIP3PBOX 10.00 0.75
> saveamberparm fep fep.prm.crd
> quit
> The next thing I want to do would be to mimic the following restraints:
> restrainAngle fep fep.103.14 fep.103.13 fep.181.1 20 124.0
> restrainAngle fep fep.103.11 fep.103.13 fep.181.1 20 127.4
> restrainAngle fep fep.103.13 fep.181.1 fep.181.2 20 93.1
> restrainAngle fep fep.103.13 fep.181.1 fep.181.23 20 98.6
> restrainAngle fep fep.103.13 fep.181.1 fep.181.39 20 106.6
> restrainAngle fep fep.103.13 fep.181.1 fep.181.55 20 103.4

This is a very old feature of tleap, and I would _not_ suggest trying to
use it. Such restraints are not specified in the topology file anymore
(and if a topology file with such restraints is used, sander and pmemd
will quit with an error message saying restraints cannot be specified in
the prmtop anymore).

> However, I am not sure how to use setangle to do this in the topology file
> derived from the above tleap script as you have suggested.

So there is a difference between what restrainAngle used to do and what
setAngle does. The former adds what is effectively a restraint but does
not exclude non-bonded interactions between the restrained angle. The
setAngle command in ParmEd actually adds the angle directly to the
topology, meaning that the atoms involved in that angle are excluded
from each others' nonbonded interactions.

If you _do_ want the exclusions, then use setAngle in ParmEd. If you do
_not_ want the exclusions, then use NMR-style restraints. ParmEd is
described in the AmberTools manual (with a description of setAngle), and
the NMR restraints are described in the Amber manual in chapter 6.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 21 2013 - 05:00:03 PST
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