AMBER Archive (2009)

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

From: Sunita Patel (sunita_iitb_at_yahoo.com)
Date: Tue Apr 28 2009 - 19:50:08 CDT

Dear Amber users,

I am new to AMBER package. I am trying to generate the coordinate and topology file from a pdb file using tleap. My leap.in file looks like this
===============================
source leaprc.ff03
set default PBradii mbondi2
m = loadpdb PsHSP_Nter.pdb
saveamberparm m hsp_eff_im.prmtop hsp_eff_im.inpcrd
quit
=================================

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.

Thanks for any help,

Best regards,
Sunita

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber