[AMBER] setting pdb file

From: Nicolas Feldman <nfeldman01.qub.ac.uk>
Date: Fri, 20 Mar 2020 18:49:46 +0000

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 - 12:00:02 PDT
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