AMBER Archive (2004)

Subject: AMBER: Question on tleap of amber8

From: Okimoto Noriaki (okimoto_at_atlas.riken.go.jp)
Date: Mon Dec 20 2004 - 03:00:38 CST

Dear AMBER Users and Developers,

I want to do a md calculation of protein-ligand complex using AMBER 8.
When I made topology file using tleap, tleap told the following message.
<><><><><><><><><><><><><><><><><><><><><><><><><><><>
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-N1-C7-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C6-N1-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
.....
....

<><><><><><><><><><><><><><><><><><><><><><><><><><><><>

After that, I add the atom types, elements, hybridizations of ligand
molecule into leaprc file,
then tleap did not tell the message above.
Besides, I found that the result of md calculation was changed by the
addition in leaprc.
I don't know how these informations (atom types, elements, and
hybridizations) are used for md calculation.
Could anyone help with this question?
Thanks.

Noriaki Okimoto

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