Dear All,
I'm getting errors while solvating ritonavir ligand.
I have checked the manual and earlier discussion but couldn't understand
why this error should appear. leap is able to create prmtop/inpcrd for the
non-solvated ligand, but fails to add water in both periodic box/oct
options.
Can you please help me understand the source of error? I want to sample
"all" possible conformations that the ligand can take at pH=7 and 0.9 %
NaCl (isotonic)
My leap input is given below.
thank you.
[r11831vd.hlogin1 [csf3] ritonavir-1W0E-dock]$ more rito-leap.in
#source leaprc.ff14
source leaprc.gaff
loadAmberParams frcmod.ionsjc_tip3p
loadamberparams ritonavir-1.frcmod
rit = loadmol2 ritonavir-1.mol2
check rit
saveoff rit ritonavir-1.lib
saveamberparm rit rit-gas.prmtop rit-gas.inpcrd
charge rit
solvatebox rit TIP3PBOX 10.0
saveamberparm rit rit-wat.prmtop rit-wat.inpcrd
quit
[r11831vd.hlogin1 [csf3] ritonavir-1W0E-dock]$ tleap -s -f rito-leap.in
-I: Adding /opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/prep to
search path.
-I: Adding /opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/lib to
search path.
-I: Adding /opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/parm to
search path.
-I: Adding /opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/cmd to
search path.
-s: Ignoring startup file: leaprc
-f: Source rito-leap.in.
Welcome to LEaP!
Sourcing: ./rito-leap.in
----- Source:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/cmd/leaprc.gaff
----- Source of
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/cmd/leaprc.gaff
done
Log file: ./leap.log
Loading parameters:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
Loading parameters:
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
Loading parameters: ./ritonavir-1.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Loading Mol2 file: ./ritonavir-1.mol2
Reading MOLECULE named RIT
Checking 'rit'....
Checking parameters for unit 'rit'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Building topology.
Building atom parameters.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 18 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
RIT 1
)
(no restraints)
Total unperturbed charge: 0.004000
Total perturbed charge: 0.004000
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/bin/teLeap: Fatal Error!
solvateBox: Argument #2 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Sun Jun 16 2019 - 02:00:02 PDT
