Thank you Prof. Case for pointing that out. It has worked for me this time.
I picked basic steps to add tip3 water model from here
<
http://ambermd.org/tutorials/advanced/tutorial33/section1.htm>which don't
seem to have that command, link to tleap.explicit.in file is broken there
<
http://ambermd.org/tutorials/advanced/tutorial33/files/tleap.explicit.in>.
I may be incorrect, but many of the tutorials are old and probably use
combinations of commands that are not relevant in Amber18.
It's not a major problem but often ends up confusing a
non-regular/non-expert user like me.
Thanks a lot anyways for the continued support.
best regards
On Sun, Jun 16, 2019 at 2:13 PM David Case <david.case.rutgers.edu> wrote:
> On Sun, Jun 16, 2019, Vaibhav Dixit wrote:
>
> >I'm getting errors while solvating ritonavir ligand.
>
> You never loaded any water leaprc files, so the TIP3PBOX unit is not
> available to you. (You can check this by typing "desc" at the tleap
> command line right before the solvateBox command.
>
> >loadAmberParams frcmod.ionsjc_tip3p
>
> Change the above to "source leaprc.water.tip3p", which will load
> solvents.lib (that has TIP3PBOX) plus the frcmod file listed above, plus
> everything else needed for tip3p water.
>
> ...good luck...dac
>
> >solvateBox: Argument #2 is type String must be of type: [unit]
> >usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
>
> p.s.: above message is tleap's way of saying that it doesn't recognize
> TIP3PBOX as a unit. It doesn't, however, tell you how to fix that
> problem....
>
>
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>
--
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
P Please consider the environment before printing this e-mail
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Received on Sun Jun 16 2019 - 10:00:01 PDT
