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
> >
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--
--
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
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Received on Fri Mar 20 2020 - 13:00:03 PDT
