Bruna,
the error suggests that the atom names within the residue do not match
the library entries.
You sent two files with the definition of residue NPH, but a different
pdb file seems to be loaded (./temp-nadph.pdb), in which a residue NPD
is defined and for which tleap finds no parameters.
-> The output you provided does not fit to your input file.
(napdha = loadpdb 2egh_edit_nadph_a.pdb)
If the residue NPD is the one, for which you have the parameters and
which is called NPH in the force field library files, you could simply
rename it in the input pdb file.
Otherwise you'd need parameters for NPD as well.
Maybe this helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 20.12.2022 um 16:45 schrieb Bruna Schuck de Azevedo via AMBER:
> 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 Wed Dec 21 2022 - 06:00:03 PST
