It looks like those are the carboxyl oxygens on the c terminal Thr groups.
Seems reasonable for leap to add them if missing.
On Fri, Mar 20, 2020, 6:31 PM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> This means a lot of hydrogen atoms being adjusted though as long as there
> are no other errors being reported it just means that the force filed
> corrected some incorrect atoms.
>
>
> Just out of curiosity, is OXT oxytocin? Furthermore, you should look into
> the pdb4amber module to prepare your PDB files before dumping them into
> leap.
>
>
> Best regards
>
> // Gustaf
>
> ________________________________
> Från: Nicolas Feldman <nfeldman01.qub.ac.uk>
> Skickat: den 20 mars 2020 21:01:15
> Till: AMBER Mailing List
> Ämne: Re: [AMBER] setting pdb file
>
> 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
> > >
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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
>
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Received on Fri Mar 20 2020 - 17:00:02 PDT
