AMBER Archive (2009)

Subject: [AMBER] sleap in AmberTools 1.3 is not working anymore for me

From: Alan (alanwilter_at_gmail.com)
Date: Tue Dec 29 2009 - 14:27:57 CST

Dear all,

This used to work pretty fine with AT 1.2, without any warning, but now with
AT 1.3 ...:

- Extract ligand DMP from 1BVG, name it Ligand.pdb

- Enter sleap terminal command and enter:
[gtkleap]$ source leaprc.ff99SB
[gtkleap]$ source leaprc.gaff
Info: ignoring unknown atom type: h
Info: while reading ANGL. Input: f c h 51.5 109.90 SOURCE2
 1 0.0000 0.0000
Info: ignoring unknown atom type: h
Info: while reading ANGL. Input: h c o 53.1 127.30 SOURCE2
 1 0.0000 0.0000
Info: ignoring unknown atom type: cb
Info: while reading DIHE. Input: X c1 cb X 2 0.000 180.000
      2.000
Info: ignoring unknown atom type: cb
Info: while reading DIHE. Input: X n1 cb X 2 0.000 180.000
      2.000
# { why these info above ?}

[gtkleap]$ set default fastbld on
[gtkleap]$ DMP = loadpdb Ligand.pdb
Warning: cannot find template for residue DMP in our library.
         You will not be able to save prmtop for this molecule.
[gtkleap]$ saveamberparm DMP Ligand_AC.prmtop Ligand_AC.inpcrd
Error: dparm pchg does not exist!

I am using a AT 1.3 compiled with intel on Mac OSX 10.6.2 64 bits.

Many thanks in advance,

Alan 

-- 
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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