Re: [AMBER] about sybylmol2 file

From: Navanath Kumbhar <>
Date: Sat, 12 Jun 2010 15:59:08 +0530

Dear sir,

I have downloaded forcefield parameter files for modified nucleosides from
amberweb sites and used in xleap and opened my mod.pdb input files.

loadamberprep WBG.prepin
loadamberparams WBG.frcmod
mod=loadpdb mod.pdb

 it gives dotts in place of atoms(means not shows bond).

I have also defined atom type and charge (as like given in tutorial) for
mod.pdb and saved mod.lib and try to get prmtop and inpcrd files for that
but it gives error as

improper torsion parameter.

when i want ot open this file again by

source leaprc.ff99SB
loadoff mod.lib
mod=loadpdb mod.pdb

it again shows dotts in place of atoms.

So please tell me there is any mistake in my saving lib file or any other.

So please tell me how can i get prmtop and inpcrd files for mod.pdb.

Thanks and reat regards
Navanth Kumbhar
On Fri, Jun 11, 2010 at 6:49 PM, case <> wrote:

> On Fri, Jun 11, 2010, Navanath Kumbhar wrote:
> >
> > 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
> See tutorial B4 for instructions on building libraries for molecules not in
> the standard database. You can't just open an arbitrary mol2 file in xleap
> --
> running antechamber is generally needed.
> You should also check the link on the Amber web site for "modified
> nucleosides
> for RNA". This site has lots of anticodonloop nucleosides; even if it
> doesn't
> have exactly the one you need, it may get you close.
> ....dac
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Received on Sat Jun 12 2010 - 03:30:03 PDT
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