HI Rana,
It seems that you have not loaded the corresponding prepi file
using the command
>> loadamberprep xyz.prepin ( or whatever the name is).
This should have been obvious because when you typed "list" there was no entry for "HEM" and only "gaff" was loaded.
Best Regards
[photo]
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in<
https://webapp.wisestamp.com/www.elvismartis.in>
Skype. adrian_elvis12<
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________________________________
From: Rana Rehan Khalid <rrkhalid.umich.edu>
Sent: 30 June 2017 05:46:42
To: AMBER Mailing List
Subject: [AMBER] kindly see the leap.log for fe---02
> source leaprc.gaff
----- Source: /home/rehan/Downloads/amber16/dat/leap/cmd/leaprc.gaff
----- Source of /home/rehan/Downloads/amber16/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/rehan/Downloads/amber16/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.8, Mar 2015)
> loadamberparams frcmod_D.hem
Loading parameters: ./frcmod_D.hem
Reading force field modification type file (frcmod)
Reading title:
Force field modifcations for all-atom heme /parametros Dario
> loadamberprep argn.in
Loading Prep file: ./argn.in
** LOOP atom FE not found - bond not formed
** LOOP atom FE not found - bond not formed
** LOOP atom FE not found - bond not formed
Discarding residue ( hemo libre ) to EOF
> list
gaff
> loadpdb hem.pdb
Loading PDB file: ./hem.pdb
Unknown residue: HEM number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: HEM sequence: 187
Created a new atom named: CAA within residue: .R<HEM 187>
Created a new atom named: CAB within residue: .R<HEM 187>
Created a new atom named: CAC within residue: .R<HEM 187>
Created a new atom named: CAD within residue: .R<HEM 187>
Created a new atom named: NA within residue: .R<HEM 187>
Created a new atom named: CBA within residue: .R<HEM 187>
Created a new atom named: CBB within residue: .R<HEM 187>
Created a new atom named: CBC within residue: .R<HEM 187>
Created a new atom named: CBD within residue: .R<HEM 187>
Created a new atom named: NB within residue: .R<HEM 187>
Created a new atom named: CGA within residue: .R<HEM 187>
Created a new atom named: CGD within residue: .R<HEM 187>
Created a new atom named: ND within residue: .R<HEM 187>
Created a new atom named: CHA within residue: .R<HEM 187>
Created a new atom named: CHB within residue: .R<HEM 187>
Created a new atom named: CHC within residue: .R<HEM 187>
Created a new atom named: CHD within residue: .R<HEM 187>
Created a new atom named: CMA within residue: .R<HEM 187>
Created a new atom named: CMB within residue: .R<HEM 187>
Created a new atom named: CMC within residue: .R<HEM 187>
Created a new atom named: CMD within residue: .R<HEM 187>
Created a new atom named: C1A within residue: .R<HEM 187>
Created a new atom named: C1B within residue: .R<HEM 187>
Created a new atom named: C1C within residue: .R<HEM 187>
Created a new atom named: C1D within residue: .R<HEM 187>
Created a new atom named: O01 within residue: .R<HEM 187>
Created a new atom named: O1A within residue: .R<HEM 187>
Created a new atom named: O1D within residue: .R<HEM 187>
Created a new atom named: C2A within residue: .R<HEM 187>
Created a new atom named: C2B within residue: .R<HEM 187>
Created a new atom named: C2C within residue: .R<HEM 187>
Created a new atom named: C2D within residue: .R<HEM 187>
Created a new atom named: O02 within residue: .R<HEM 187>
Created a new atom named: O2A within residue: .R<HEM 187>
Created a new atom named: O2D within residue: .R<HEM 187>
Created a new atom named: C3A within residue: .R<HEM 187>
Created a new atom named: C3B within residue: .R<HEM 187>
Created a new atom named: C3C within residue: .R<HEM 187>
Created a new atom named: C3D within residue: .R<HEM 187>
Created a new atom named: C4A within residue: .R<HEM 187>
Created a new atom named: C4B within residue: .R<HEM 187>
Created a new atom named: C4C within residue: .R<HEM 187>
Created a new atom named: C4D within residue: .R<HEM 187>
Created a new atom named: NC within residue: .R<HEM 187>
Created a new atom named: FE within residue: .R<HEM 187>
total atoms in file: 45
The file contained 45 atoms not in residue templates
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Received on Thu Jun 29 2017 - 21:00:03 PDT
