Elvis
source leaprc.gaff
loadamberparams heme.frcmod
loadamberprep heme_all.in
list
HEM GAFF
after that i load the molecules it show o01 and o02 new atom type that are
not in the prototype is this file ok for fe---o2 bonded type if yes then
which atom i replace in the pdb file to match the files thanks
On Thu, Jun 29, 2017 at 11:58 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> 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<https://webapp.wisestamp.com/#>
>
>
> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> in/elvisadrianmartis/>
>
>
>
>
>
> ________________________________
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 29 2017 - 21:30:02 PDT
