AMBER Archive (2008)

Subject: RE: AMBER: NAD+ parameters problem using tleap

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Oct 17 2008 - 13:16:41 CDT

Hi Dmitri,

 

These warnings are innocuous. They originate from inside leap where it has
its own drawing / minimization routines etc for relaxing structures etc.
These don't end up in the prmtop and inpcrd file so can safely be ignored.

 

All the best

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Dmitri Nilov
Sent: Friday, October 17, 2008 9:25 AM
To: amber_at_scripps.edu
Subject: AMBER: NAD+ parameters problem using tleap

 

Hi all!

I want to simulate protein with NAD+ cofactor,

so I try to use NAD+ parameters contributed by Ross Walker.

I launch tleap using leaprc.ff99SB,

then load parameter files (loadamberparams frcmod.NAD+, then loadoff
NAD+.lib).

When I load pdb of my protein with NAD+ or just pdb of NAD+ I get message:

 

> mol = loadpdb 2nac_ndp.pdb
Loading PDB file: ./2nac_ndp.pdb
  Added missing heavy atom: .R<CALA 393>.A<OXT 11>
  Added missing heavy atom: .R<CALA 786>.A<OXT 11>
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C18-N7-*
+--- With Sp2 - 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: *-C21-N6-*
+--- With Sp2 - 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: *-C16-N6-*
+--- With Sp2 - 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: *-C15-N6-*
+--- With Sp3 - 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: *-C18-N7-*
+--- With Sp2 - 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: *-C21-N6-*
+--- With Sp2 - 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: *-C16-N6-*
+--- With Sp2 - 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: *-C15-N6-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
  total atoms in file: 6975
  Leap added 7616 missing atoms according to residue templates:
       2 Heavy
       7614 H / lone pairs
>

 

After unit checking ("check mol") tleap says that unit is OK.

I`ve tried to simulate with obtained .prmtop and .inpcrd files and
simulation results seems to be OK.
Residue name in my pdb is NDP and all NDP atom names and atom order in my
pdb match those in nad+.lib

So, are there any reasons to worry about tleap warnings?

 

Thanks,

Dmitri Nilov

Lomonosov Moscow State University

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