Re: [AMBER] problem running antechamber - amber Version 10

From: FyD <>
Date: Wed, 25 Sep 2013 17:02:51 +0200

Dear Monica,

Your input molecule is far too big...

 From what I saw when loading your molecule into vmd this is a
glycopeptide with some organic functions or modified amino-acid

I think you should split this molecule into elementary building blocks
and carefully pay attention how to connect these elementary building

You can find a similar project in R.E.DD.B. by C. Cezard et al.

All is done with R.E.D. Server - and as you can see F-85 is about
Glucose based (alpha-1,4) oligomers with new organic functions and a
peptide region...

regards, Francois

> I am trying to generate the topology file for a molecule of 8
> glucose residues with 3 peptides attached to it. My purpose is to
> build a cellulose nanocrystal with peptides and minimize and carry
> out an MD simulation with Amber software.
> I gave the following command:
> antechamber -i new-chemx.pdb -fi pdb -o new-chemx.mol2 -fo mol2 -c bcc
> And I got the following error messages:
> The atom number exceeds the MAXATOM, reallocate memory
> Info: the bond number exceeds MAXBOND, reallocate memory automatically
> Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> (aromatic double)Error: cannot run
> "/home/glenn/amber10_distribution/amber10/bin/bondtype -j full -i
> judgebondtype() of antechamber.c properly, exit
> I attached my input files. Please let me know what causes this problem.

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Received on Wed Sep 25 2013 - 08:30:03 PDT
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