I never set the force field haha.
Thank you.
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: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Friday, March 20, 2020 7:29 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] setting pdb file
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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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Received on Fri Mar 20 2020 - 13:00:02 PDT
