Hi,
I want to do a simulation where NADPH is one of the ligands.
I have a pdb file with just the NADPH and found its parameters at
http://amber.manchester.ac.uk/, the Ryde one.
When I try to run tleap, I get a warning:
""
>tleap -f join_nadph_tleap.in
-I: Adding /Home/Softwares/test/amber22/dat/leap/prep to search path.
-I: Adding /Home/Softwares/test/amber22/dat/leap/lib to search path.
-I: Adding /Home/Softwares/test/amber22/dat/leap/parm to search path.
-I: Adding /Home/Softwares/test/amber22/dat/leap/cmd to search path.
-f: Source join_nadph_tleap.in.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./join_nadph_tleap.in
----- Source: /Home/Softwares/test/amber22/dat/leap/cmd/leaprc.protein.ff19SB
----- Source of /Home/Softwares/test/amber22/dat/leap/cmd/leaprc.protein.ff19SB done
Log file: ./leap.log
Loading parameters: /Home/Softwares/test/amber22/dat/leap/parm/parm19.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB
Loading parameters: /Home/Softwares/test/amber22/dat/leap/parm/frcmod.ff19SB
Reading force field modification type file (frcmod)
Reading title:
ff19SB AA-specific backbone CMAPs for protein 07/25/2019
Loading library: /Home/Softwares/test/amber22/dat/leap/lib/amino19.lib
Loading library: /Home/Softwares/test/amber22/dat/leap/lib/aminoct12.lib
Loading library: /Home/Softwares/test/amber22/dat/leap/lib/aminont12.lib
----- Source: /Home/Softwares/test/amber22/dat/leap/cmd/leaprc.gaff2
----- Source of /Home/Softwares/test/amber22/dat/leap/cmd/leaprc.gaff2 done
Log file: ./leap.log
Loading parameters: /Home/Softwares/test/amber22/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
Loading Prep file: ./nadph.prep
/Home/Softwares/test/amber22/bin/teLeap: Warning!
Per-line charges being overridden by CHARGE block in NADPH, Total charge -4, AMBER 5.0 compatible; U. Ryde, to be published, 22/4-98
/Home/Softwares/test/amber22/bin/teLeap: Warning!
Per-line charges being overridden by CHARGE block in NADPH, Total charge -3, AMBER 5.0 compatible; U. Ryde, to be published, 22/4-98
Loading parameters: ./nad.frcmod
Reading force field modification type file (frcmod)
Reading title:
#Special force constants for NAD+, NADH, NADP+, and NADPH; Ulf Ryde, 24 April, 1998
Loading PDB file: ./temp-nadph.pdb
/Home/Softwares/test/amber22/bin/teLeap: Warning!
Unknown residue: NPD number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
/Home/Softwares/test/amber22/bin/teLeap: Warning!
-no luck
Creating new UNIT for residue: NPD sequence: 3001
Created a new atom named: PA within residue: .R<NPD 3001>
Created a new atom named: O1A within residue: .R<NPD 3001>
Created a new atom named: O2A within residue: .R<NPD 3001>
Created a new atom named: O5B within residue: .R<NPD 3001>
Created a new atom named: C5B within residue: .R<NPD 3001>
Created a new atom named: C4B within residue: .R<NPD 3001>
Created a new atom named: O4B within residue: .R<NPD 3001>
Created a new atom named: C3B within residue: .R<NPD 3001>
Created a new atom named: O3B within residue: .R<NPD 3001>
Created a new atom named: C2B within residue: .R<NPD 3001>
Created a new atom named: O2B within residue: .R<NPD 3001>
Created a new atom named: C1B within residue: .R<NPD 3001>
Created a new atom named: N9A within residue: .R<NPD 3001>
Created a new atom named: C8A within residue: .R<NPD 3001>
Created a new atom named: N7A within residue: .R<NPD 3001>
Created a new atom named: C5A within residue: .R<NPD 3001>
Created a new atom named: C6A within residue: .R<NPD 3001>
Created a new atom named: N6A within residue: .R<NPD 3001>
Created a new atom named: N1A within residue: .R<NPD 3001>
Created a new atom named: C2A within residue: .R<NPD 3001>
Created a new atom named: N3A within residue: .R<NPD 3001>
Created a new atom named: C4A within residue: .R<NPD 3001>
Created a new atom named: O3 within residue: .R<NPD 3001>
Created a new atom named: PN within residue: .R<NPD 3001>
Created a new atom named: O1N within residue: .R<NPD 3001>
Created a new atom named: O2N within residue: .R<NPD 3001>
Created a new atom named: O5D within residue: .R<NPD 3001>
Created a new atom named: C5D within residue: .R<NPD 3001>
Created a new atom named: C4D within residue: .R<NPD 3001>
Created a new atom named: O4D within residue: .R<NPD 3001>
Created a new atom named: C3D within residue: .R<NPD 3001>
Created a new atom named: O3D within residue: .R<NPD 3001>
Created a new atom named: C2D within residue: .R<NPD 3001>
Created a new atom named: O2D within residue: .R<NPD 3001>
Created a new atom named: C1D within residue: .R<NPD 3001>
Created a new atom named: N1N within residue: .R<NPD 3001>
Created a new atom named: C2N within residue: .R<NPD 3001>
Created a new atom named: C3N within residue: .R<NPD 3001>
Created a new atom named: C7N within residue: .R<NPD 3001>
Created a new atom named: O7N within residue: .R<NPD 3001>
Created a new atom named: N7N within residue: .R<NPD 3001>
Created a new atom named: C4N within residue: .R<NPD 3001>
Created a new atom named: C5N within residue: .R<NPD 3001>
Created a new atom named: C6N within residue: .R<NPD 3001>
Created a new atom named: P2B within residue: .R<NPD 3001>
Created a new atom named: O1X within residue: .R<NPD 3001>
Created a new atom named: O2X within residue: .R<NPD 3001>
Created a new atom named: O3X within residue: .R<NPD 3001>
total atoms in file: 48
The file contained 48 atoms not in residue templates
> quit
""
The join_nadph_tleap.in file:
""
source leaprc.protein.ff19SB
source leaprc.gaff2
loadamberprep nadph.prep
loadamberparams nad.frcmod
napdha = loadpdb 2egh_edit_nadph_a.pdb
#saveamberparm mol nadph_a_h.top nadph_a_h.cord
#savepdb mol nadph_a_h_out.pdb
#quit
""
It seems that to be a problem with the atom names from the pdb file and the ones from the prep file (both files attached).
Did someone have a similar experience? Could the force field choice have something to do with it? Any suggestions to overcome such warning and proceed with the simulation?
Kind regards,
Bruna
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Received on Tue Dec 20 2022 - 08:00:02 PST
