Yes, if you are using a protein with "standard residiues" you should infidelity load the force field (parameters) before loading the PDB file, otherwise everything in the PDB file will be considered as "foreign".
Quite right, OXT is an atom label. I was just curious.
Best regards
// Gustaf
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Från: Nicolas Feldman <nfeldman01.qub.ac.uk>
Skickat: den 20 mars 2020 23:44:02
Till: AMBER Mailing List
Ämne: Re: [AMBER] setting pdb file
Hi Gustaf,
Thank you. Actually what I tried to do was to prepare my pdb protein before adding it to leap. But I've never realized that I have to added the field force before load the molecule.
For what I understand of the Amber manual OXT is atom un this case rather than a molecule
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: Gustaf Olsson <gustaf.olsson.lnu.se>
Sent: Friday, March 20, 2020 10:31 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] setting pdb file
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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
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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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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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 - 16:00:03 PDT
