AMBER Archive (2009)

Subject: [AMBER] tleap maximum coordination exceeded

From: Jack Shultz (js_at_drugdiscoveryathome.com)
Date: Tue Nov 17 2009 - 10:52:20 CST

Dear Amber users,

Any suggestions on how to resolve this issue? I am trying to use tleap
to fill in missing residues. I have tried it with both pdb and mol2
format files

tleap -s -f /usr/local/antechamber-1.27/dat/leap/cmd/leaprc.ff99
str1=loadpdb fzd8min_renum_SS2.pdb

It aborted with this message
Bond: Maximum coordination exceeded on .R<GLU 276>.A<H 2>
      -- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<NGLU 32>.A<OE2 15> .R<GLU 276>.A<H 2>
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 444
!FATAL: Message: bondAtomProblem found
!
!ABORTING.

Also when I try using mol2 file
> str1 = loadmol2 receptor2.mol2
Loading Mol2 file: ./receptor2.mol2
Reading MOLECULE named receptor2.mol2

For a list of the current aliases, type "alias".
> savepdb
savePdb: Improper number of arguments!
usage: savePdb <object> <filename>
> savepdb str1 test.pdb
savePdb: Argument #1 is type String must be of type: [unit]
usage: savePdb <object> <filename>

what's wrong with what I'm doing? 

-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org

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