AMBER Archive (2009)

Subject: Re: [AMBER] tleap maximum coordination exceeded

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Nov 17 2009 - 14:18:20 CST

Dear Jack,

- This is difficult to help you without looking at your structure.

- You might update your LEaP version using that from the AmberTools
1.2; you will find the savemol2 command in that LEaP version (for
instance).

regards, Francois

> 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

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