AMBER Archive (2009)

Subject: RE: [AMBER] Nonterminal, was not found in name map

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 28 2009 - 21:49:50 CDT

Hi Sunita,

> Though the tleap program created the coordinate and topology, it gave
> some unwanted message in the leap.log file as given below.
>
> **********************************************
> > set default PBradii mbondi2
> Using H(N)-modified Bondi radii
> > m = loadpdb PsHSP_Nter.pdb
> Loading PDB file: ./PsHSP_Nter.pdb
> Enter zPdbReadScan from call depth  0.
> Exit  zPdbReadScan from call depth  0.
> Matching PDB residue names to LEaP variables.
> (Residue 0: ACE, Terminal/beginning, was not found in name map.)
> (Residue 1: SER, Nonterminal, was not found in name map.)
> (Residue 2: LEU, Nonterminal, was not found in name map.)
> (Residue 3: ILE, Nonterminal, was not found in name map.)
> (Residue 4: PRO, Nonterminal, was not found in name map.)
> (Residue 5: SER, Nonterminal, was not found in name map.)
> (Residue 6: PHE, Nonterminal, was not found in name map.)
> *********************************************************************
> Could anybody tell whether my coordinate file and topology files are
> correct to proceed to the next step.

If this is just seen in the leap.log file you are safe to ignore it. I have
seen it many times myself without any issues. Leap tends to be VERY verbose
in the leap.log file. I am actually not sure what the origin of this warning
actually is. Perhaps Wei can comment some more. Assuming you do not see
messages about unknown residues inside leap itself you should be fine.

All the best
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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