Re: [AMBER] Help needed regarding Ligand Protein MD studies

From: Ruchika Bhat <ruchikabhat31.gmail.com>
Date: Sat, 8 Nov 2014 10:47:27 -0500

Thank you Sir for your help.

It worked.

I found that a .dat file was not being loaded when I tried to generate crd
and top and after loading it the atom types were recognized.

Once again thanking you for your generous help and valuable guidance.

Best Regards,
Ruchika

On Sat, Nov 8, 2014 at 10:14 AM, David A Case <case.biomaps.rutgers.edu>
wrote:

> On Fri, Nov 07, 2014, Ruchika Bhat wrote:
>
> > Tried doing with mol2 file also but same error.
> >
> > > a= loadpdb pdb1_10854218DOCK.pdb
> > Loading PDB file: ./pdb1_10854218DOCK.pdb
> > Created a new atom named: OXT within residue: .R<CYS 212>
> > ERROR: Comparing atoms
> > .R<CYS 212>.A<C 10>,
> > .R<DRG 1>.A<H 2>,
> > .R<DRG 1>.A<H1 3>, and
> > .R<DRG 1>.A<H2 4>
> > to atoms
> > .R<DRG 1>.A<C1 5>,
> > .R<CYS 212>.A<C 10>,
> > .R<DRG 1>.A<H2 4>, and
> > .R<DRG 1>.A<H 2>
> > This error may be due to faulty Connection atoms.
> > !FATAL ERROR----------------------------------------
> > !FATAL: In file [chirality.c], line 140
> > !FATAL: Message: Atom named C1 from DRG did not match !
> > !
> > !ABORTING.
>
> It looks like you may be missing a TER card between the protein and the
> ligand
> in pdb1_10854218DOCK.pdb.
>
> If that doesn't help, we'd need to see all the files for a small example
> that
> illustrates the problem, and allows us to reproduce it.
>
> ....dac
>
>
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Received on Sat Nov 08 2014 - 08:00:02 PST
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