[AMBER] Tutorial A08

From: Nicolas Feldman <nfeldman01.qub.ac.uk>
Date: Fri, 28 Feb 2020 16:23:16 +0000


I'm doing the tutorial A08 (https://ambermd.org/tutorials/advanced/tutorial8/loop3.htm), but when I follow the instruction when doing:
> loadoff MG.off.txt
Loading library: ./MG.off.txt
> mol = loadpdb wt1mg.pdb
The output should be:
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

Could it be that I'm saving the MG.off as a txt or something similar or it just that the tutorial is for a former version,


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 Feb 28 2020 - 08:30:01 PST
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