Dear Amber community,
I want to do simulation of modified nuclesodies with anticodonloop
structures by using sybyl mol2 file as input file format. I opened this file
in xleap by using gaff force field but when i go to save it it gives
for atom: .R<UNK0001 1 >. A < H108 285 > could not find type : H
SO which force field i can use for to get top and crd files or any other
procedure for that.
Thanks and great regards
from
Navanath Kumbhar
On Fri, Jun 11, 2010 at 6:39 AM, case <case.biomaps.rutgers.edu> wrote:
> 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".
>
> ....dac
>
>
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Received on Fri Jun 11 2010 - 03:30:04 PDT
