[AMBER] problem adding MG.off file

From: Nicolas Feldman <nfeldman01.qub.ac.uk>
Date: Mon, 2 Mar 2020 12:31:19 +0000


I'm doing the A08 tutorial (https://ambermd.org/tutorials/advanced/tutorial8/loop3.htm)

But when adding the MG.off file instead of having this output:

Loading PDB file: ./wt1mg.pdb
Added missing heavy atom: .R<CGLN 154>.A<OXT 18>
total atoms in file: 1189
Leap added 1192 missing atoms according to residue templates:
1 Heavy
1191 H / lone pairs

But in my case is:

Loading PDB file: ./wt1mg.pdb
Warning: Unknown residue: CYS number: 0 type:
Terminal/beginning ..relaxing end constraints to try for a dbase match
Warning: -no luck

  total atoms in file: 1189
The file contained 1188 atoms not in residue templates

Any idea why tleap is not recognizing this file ?

There has been any changes on the way of open and reading files in tleap since the tutorial come up ?

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

AMBER mailing list
Received on Mon Mar 02 2020 - 05:00:01 PST
Custom Search