I added the 'source leaprc.protein.ff14SB' as Daniel suggest and work
And got the right output:
Loading PDB file: ./5ixhnew.pdb
Added missing heavy atom: .R<CTHR 159>.A<OXT 15>
Added missing heavy atom: .R<CTHR 320>.A<OXT 15>
total atoms in file: 2396
Leap added 2402 missing atoms according to residue templates:
2 Heavy
2400 H / lone pairs
Nicolas Feldman
PhD Student
The Wellcome-Wolfson Institute for Experimental Medicine
Queen's University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL
-----Original Message-----
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Friday, March 20, 2020 7:56 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] setting pdb file
This message is from an external sender. Please take care when responding, clicking links or opening attachments.
maybe share the leap.log file
On Fri, Mar 20, 2020 at 3:29 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Sounds like maybe you forgot to load a parameter set prior to loading
> the PDB, e.g. 'source leaprc.protein.ff14SB' or something.
>
> -Dan
>
> On Fri, Mar 20, 2020 at 2:50 PM Nicolas Feldman <nfeldman01.qub.ac.uk>
> wrote:
> >
> > Hello I'm trying to minimize and set the pdb file for molecular dynamics.
> >
> > I did: pdb4amber -i 5ixh.pdb -o 5ixhnew.pdb --reduce --dry -d -y -p
> > But when I open the new pdb file in tleap I have the following
> > output
> error:
> > total atoms in file: 2396
> > The file contained 2396 atoms not in residue templates
> >
> > Any idea what im doing wrong ?
> >
> > Kind regards,
> >
> >
> > Nicolas Feldman
> > PhD Student
> > The Wellcome-Wolfson Institute for Experimental Medicine Queen's
> > University of Belfast; 97 Lisburn Rd. Belfast, UK BT9 7BL
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Carlos Simmerling, Ph.D. (he, him, his)
Marsha Laufer Endowed Professor of Physical and Quantitative Biology Professor, Department of Chemistry Associate Director, Laufer Center for Physical and Quantitative Biology Room 119 Laufer Center, Stony Brook University, Stony Brook, NY 11794-5115
http://www.simmerlinglab.org
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 20 2020 - 13:30:02 PDT
