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.
Thanks a lot.
Best Regards,
Moitrayee
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Received on Fri Nov 15 2013 - 16:00:02 PST
