I tried this, but it failed. See below:
>mol1 = loadmol2 CHEMBL.mol2
>mol2 = loadpdb CHEMBL_noH.pdb
Unknown residue: CHE number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: CHE sequence: 0
Created a new atom named: C9 within residue: .R<CHE 0>
Created a new atom named: C10 within residue: .R<CHE 0>
Created a new atom named: C11 within residue: .R<CHE 0>
Created a new atom named: C12 within residue: .R<CHE 0>
Created a new atom named: C13 within residue: .R<CHE 0>
Created a new atom named: C14 within residue: .R<CHE 0>
Created a new atom named: S1 within residue: .R<CHE 0>
Created a new atom named: C15 within residue: .R<CHE 0>
Created a new atom named: N2 within residue: .R<CHE 0>
Created a new atom named: H2 within residue: .R<CHE 0>
Created a new atom named: N3 within residue: .R<CHE 0>
Created a new atom named: H11 within residue: .R<CHE 0>
Created a new atom named: C16 within residue: .R<CHE 0>
Created a new atom named: N5 within residue: .R<CHE 0>
Created a new atom named: C19 within residue: .R<CHE 0>
Created a new atom named: H5 within residue: .R<CHE 0>
Created a new atom named: N4 within residue: .R<CHE 0>
Created a new atom named: C18 within residue: .R<CHE 0>
Created a new atom named: H22 within residue: .R<CHE 0>
Created a new atom named: C17 within residue: .R<CHE 0>
Created a new atom named: C22 within residue: .R<CHE 0>
Created a new atom named: N6 within residue: .R<CHE 0>
Created a new atom named: H13 within residue: .R<CHE 0>
Created a new atom named: C20 within residue: .R<CHE 0>
Created a new atom named: C21 within residue: .R<CHE 0>
Created a new atom named: O2 within residue: .R<CHE 0>
Created a new atom named: H18 within residue: .R<CHE 0>
Created a new atom named: C8 within residue: .R<CHE 0>
Created a new atom named: N1 within residue: .R<CHE 0>
Created a new atom named: H7 within residue: .R<CHE 0>
Created a new atom named: O1 within residue: .R<CHE 0>
Created a new atom named: C7 within residue: .R<CHE 0>
Created a new atom named: C2 within residue: .R<CHE 0>
Created a new atom named: C1 within residue: .R<CHE 0>
Created a new atom named: C3 within residue: .R<CHE 0>
Created a new atom named: C4 within residue: .R<CHE 0>
Created a new atom named: C5 within residue: .R<CHE 0>
Created a new atom named: C6 within residue: .R<CHE 0>
Created a new atom named: Cl1 within residue: .R<CHE 0>
total atoms in file: 39
The file contained 39 atoms not in residue templates
Then, when I did savePdb, it saved a file without hydrogens. Where am I going wrong here? There is no error when I load my mol2 file...
Thanks
Amir
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Friday, July 15, 2016 8:12:18 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Generating a HETATM database to use with reduce
On Fri, Jul 15, 2016, Kucharski Jr., Amir N wrote:
>
> What commands do I need to use in tleap in order to do this? I know how
> to load the mol2 and pdb files, but what is the command to save a new
> pdb file with the proper hydrogen configurations?
savePdb (tleap automatically adds missing hydrogens; there is no special
command to do that)
....dac
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Received on Fri Jul 15 2016 - 10:00:02 PDT
