Re: [AMBER] about sybylmol2 file

From: case <>
Date: Thu, 10 Jun 2010 21:09:04 -0400

On Thu, Jun 10, 2010, Navanath Kumbhar wrote:
> I want to creates .prepin and frcmod files for modified nucleosides by using
> antechamber, for that i have taken sybylmol2 file as input for antechamber,
> but it gives error as follows:
> $ antechamber -i wym.mol2 -fi mol2 -o wym.prepin -fo prepi -c bcc -s 2
> The atom number exceeds the MAXATOM,

How many atoms are in your modified nucleoside? Remember that antechamber
is designed for single residues, or for drug-sized molecules.

> Total number of electrons: 1383; net charge: 0
> INFO: Number of electrons is odd: 1383

Antechamber only works for closed shell molecules. Do you have a net charge
on your input molecule? If so, you must use the "-nc" option.

Please work on smaller systems first, if at all possible. 1400 electrons is
a *lot*. Also, making parameters for *residues* (that will be linked to
others as a part of a polymer) is more complex than for an isolated molecule.

Also, be sure to check if what you need has already been done: the Amber web
site has links to "modified nucleosides" and to "REDDB".


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Received on Thu Jun 10 2010 - 18:30:03 PDT
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