On Fri, Nov 15, 2013 at 6:59 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
> I am planning to run an MD simulation with a pentacoordinated HEME-HIS. I
> am
> using the heme-all parameters (which is for coordinated sytem) and trying
> to use
> a patch from CHARMM to build in additional bonds, angles etc. and delete
> some
> angles using tleap.
>
> However, it seems that tleap has no function to add a new angle or delete
> one. I
> cn easily add a bond but not new angles, dihedrals. The patch is as
> follows:
> DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND
> BOND 1NE2 2FE
> ANGLE 1CD2 1NE2 2FE 1CE1 1NE2 2FE 1NE2 2FE 2NA 1NE2 2FE 2NB
> ANGLE 1NE2 2FE 2NC 1NE2 2FE 2ND
>
> When I translate this to tleap:
>
> fep = loadpdb fep.prm.pdb
> delete angle fep.181.NA fep.181.FE fep.181.NC fep.181.NB fep.181.FE
> fep.181.ND
> bond fep.103.NE2 fep.181.FE
> angle fep.103.CD2 fep.103.NE2 fep.181.FE fep.103.CE1 fep.103.NE2
> fep.181.FE
> fep.103.NE2 fep.181.FE fep.181.NA fep.103.NE2 fep.181.FE fep.181.NB
> angle fep.103.NE2 fep.181.FE fep.181.NC fep.181.NE2 fep.181.FE
> fep.181.ND
>
>
> addions fep Na+ 0
> solvatebox fep TIP3PBOX 10.00 0.75
> saveamberparm fep fep.prm.top fep.prm.crd
> quit
>
> However, there is no angle command in tleap. I am a little confused as to
> how to
> implement this. Any suggestion would be very much appreciated.
>
As Dave mentioned, there is no 'angle' command in tleap.
You can create the topology file in tleap _without_ the angle parameters
and then use the setAngle command in ParmEd to add the angles afterwards.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Nov 17 2013 - 09:00:03 PST
