Dear shivangi agarwal,
There's no need to create a ZN residue by yourself, it's already available for you after sourcing the cmd file "leaprc.water.tip3p", together with Na+ and other ions and solvents...
The issue you are facing is because leap first search for requested files by cmd (*.lib, *.frcmod, etc) in the working directory, if they are there, then it will use then... if they aren't then it will search in the AMBER path (or additional in paths, see command "addPath")... so leap is reading your custom "atomic_ions.lib" library, which only has the ZN residue in it.
To solve the problem, remove you custom "atomic_ions.lib" library from your working directory and try again...
Best,
Matias
----- Mensaje original -----
De: "shivangi agarwal" <shiviagarwalpharma.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Lunes, 29 de Julio 2019 1:51:30
Asunto: Re: [AMBER] Error in preparing system using AmberTools19
Hello
As per the above suggestions , I have run simple system and slowly
increased complexity, for e.g. I first run only protein, then
protein_ligand complex and then protein_ligand with zinc.
I came to know that when there is zinc, then it is causing problem to me
during addition of ions (addions complex Na+ 6), rest in two systems
(protein and protein-ligand complex), I successfully generated parameters.
The commands are as:
*####for protein#####*
tleap
source leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.gaff
protein=loadpdb protein.pdb
list
saveAmberparm protein protein.prmtop protein.inpcrd
solvateBox protein TIP3PBOX 10.0
list
charge protein
addions protein Na+ 8
saveAmberParm protein protein-box.prmtop protein-box.inpcrd
*#for protein-ligand complex####*
antechamber -i Ligand_42_complex.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc
-s 2
parmchk2 -i ligand.mol2 -f mol2 -o ligand.frcmod
tleap
source leaprc.gaff
LIG=loadmol2 ligand.mol2
list
check LIG
loadAmberParams ligand.frcmod
saveoff LIG ligand.lib
savepdb LIG ligand-antechamber.pdb
saveAmberParm LIG ligand.prmtop ligand.inpcrd
quit
tleap
source leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.gaff
loadAmberParams ligand.frcmod
loadoff ligand.lib
complex=loadpdb complex_42_final_2_noH_no_zn.pdb
saveAmberParm complex complex.prmtop complex.inpcrd
solvateBox complex TIP3PBOX 10.0
charge complex
addions complex Na+ 8
saveAmberParm complex complex-box.prmtop complex-box.inpcrd
*###for protein ligand complex with zinc##########*
antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2
parmchk2 -i ligand.mol2 -f mol2 -o ligand.frcmod
tleap
source leaprc.gaff
LIG=loadmol2 ligand.mol2
list
check LIG
loadAmberParams ligand.frcmod
saveoff LIG ligand.lib
savepdb LIG ligand-antechamber.pdb
saveAmberParm LIG ligand.prmtop ligand.inpcrd
quit
tleap
i = createAtom ZN Zn2+ 2.0
set i element "Zn"
set i position { 0 0 0 }
r = createResidue ZN
add r i
ZN = createUnit ZN
add ZN r
saveOff ZN ./atomic_ions.lib
quit
tleap
source leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.gaff
loadAmberParams ligand.frcmod
loadoff atomic_ions.lib
loadoff ligand.lib
complex=loadpdb pdb_complex_18_noH.pdb
saveAmberParm complex complex.prmtop complex.inpcrd
savepdb complex complex.pdb
solvateBox complex TIP3PBOX 10.0
charge complex
*addions complex Na+ 1*
Error: addIons: Argument #2 is type String must be of type: [unit]
addIons unit ion1 #ion1 [ion2 #ion2]
UNIT _unit_
UNIT _ion1_
NUMBER _#ion1_
UNIT _ion2_
NUMBER _#ion2_
Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addIons, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.
Also, attaching leap.log file of each system.
Kindly look into this and suggest.
On Thu, Jul 25, 2019 at 1:01 AM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> just one more thing... don't forget to close (quit) the leap session and
> re-open it again to "clean" the software memory... otherwise you may run
> into the same issues due to some stored variables...
>
> Matias
>
> ----- Mensaje original -----
> De: "Matias Machado" <mmachado.pasteur.edu.uy>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> CC: "David Case" <david.case.rutgers.edu>
> Enviados: Miércoles, 24 de Julio 2019 16:21:35
> Asunto: Re: [AMBER] Error in preparing system using AmberTools19
>
> After digging deeper into your "leap.log" I may found the problem...
>
> > i = createAtom ZN Zn2+ 2.0
> > set i element "Zn"
> > set i position { 0 0 0 }
> > r = createResidue ZN
> > add r i
> > ZN = createUnit ZN
> > add ZN r
> > saveOff ZN ./atomic_ions.lib
> Saving ZN.
>
> So it seem you've been doing a lot of custom "trial and error" stuff...
>
> Hence I recommend you to remove the leap.log file (because it's very
> messy) and start from scratch with you system setup...
>
> First load the parameter in the proper way (e.i. by using the cmd files),
> then load the coordinates and at last add solvent and ions...
>
> # Example after decoding your log file:
>
> # Load parameters
> source leaprc.protein.f14SB
> source leaprc.water.tip3p
> source leaprc.gaff
>
> # Load coordinate
> com=loadpdb complex_42_final_2_noH.pdb
>
> # Solvate and add ions
> solvateBox com TIP3PBOX 10.0
> addIonsRand com Na+ 0
>
> # Save topology and coordinates in netcdf
> saveAmberParmNetcdf com XXX.prmtop XXX.ncrst
>
> Best,
>
> Matias
>
> PS: this is a guess, I don't know what's in you system, so there may be
> missing parameters to check...
>
> ----- Mensaje original -----
> De: "Matias Machado" <mmachado.pasteur.edu.uy>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> CC: "David Case" <david.case.rutgers.edu>
> Enviados: Miércoles, 24 de Julio 2019 15:58:53
> Asunto: Re: [AMBER] Error in preparing system using AmberTools19
>
> There is something wrong with your installation/implementation of AMBER
> Tools 19, because the "leaprc.water.tip3p" must load the Na+ residue from
> the library "atomic_ions.lib"... I tied to do it myself and it worked
> perfectly...
>
> Indeed, the "atomic_ions.lib" is being loaded from your working directory
> (./) instead of the AMBER database, which in your case I guess is located
> at /home/ravi/anaconda3/dat/leap/lib, and it seems to only contain the ZN
> residue, that's rare...
>
> Best,
>
> Matias
>
> ----- Mensaje original -----
> De: "shivangi agarwal" <shiviagarwalpharma.gmail.com>
> Para: "David Case" <david.case.rutgers.edu>, "AMBER Mailing List" <
> amber.ambermd.org>
> Enviados: Miércoles, 24 de Julio 2019 0:50:12
> Asunto: Re: [AMBER] Error in preparing system using AmberTools19
>
> I have attached the leap.log file.
> I checked using list command
> *com* is there
> but as I am getting error during addition of Na+,
> So Na+ is not there.
> Kindly look into the leap.log file and suggest
>
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Received on Sun Jul 28 2019 - 23:00:02 PDT
