Hi,
The Solvate.sh script is really just a brute force trial and error approach
to getting a target number of waters that uses a steepest-descent-like
algorithm (not really optimal). You may want to try using something like
packmol as well.
First, make sure you are using the latest version:
https://github.com/drroe/Solvate.sh
Second, the default tolerance is really too small. You probably can/should
increase it to something like 10. I put it in because the brute force
approach has its limits due to geometry (sometimes no matter how small the
increase/decrease in unit cell size, you will end up adding/removing more
than one water). The idea is that any “bubbles” left by this will disappear
during careful relaxation.
Hope this helps/clears some things up.
-Dan
On Fri, Jun 18, 2021 at 5:08 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear All,
> In the absence of examples for the "remove" command in the manual and in
> the archive and failure to use solvate.sh script, I saved a pdb and simply
> used the parmed to strip the last water molecule (residue) to match the
> topology with another state.
> The equilibration stage went through without errors and production MD is
> running.
> It would help if someone could comment if this approach is acceptable.
> I read the solvate.sh script but couldn't understand the approach/algorithm
> it uses to select water(s) for removal.
> Thus I'm unable to make a judgement if the solvate.sh script would be more
> suitable than a random cheery(water)-picking that I did using parmed.
> Looking forward to valuable suggestions from the list.
> thank you and best regards.
>
>
> On Thu, Jun 17, 2021 at 10:53 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
> > Dear All,
> > I'm getting the following error while trying to control the number of
> > waters that are save in prmtop/inpcrd. For this, I'm trying to use the
> > solvate.sh script as mentioned in Amber20 manual section 13.7.4. The
> input
> > file for solvate.sh is given below.
> > I tried modifications like the following in the resulting temp.leap.in
> > remove mol.6451
> > remove mol.6451.O
> > Can you please suggest what is the correct usage of the remove command
> > which seems to cause the following error?
> > thanks in advance and best regards.
> >
> > Error at the stage of removing extra water
> > -------------
> >
> > (Replacing solvent molecule)
> > Placed Na+ in mol at (-9.57, -20.67, -5.96).
> >
> > Done adding ions.
> >
> > /home/user/Installations/amber18/bin/teLeap: Fatal Error!
> > remove: Argument #2 is type Double must be of type: [molecule residue
> atom]
> > usage: remove <unit/residue/atom> <unit/residue/atom>
> >
> > Exiting LEaP: Errors = 1; Warnings = 5; Notes = 1.
> > --------------
> >
> > input for solvate.sh
> > --------------
> > # Target number of waters
> > target 6302
> > # Initial guess for buffer
> > buffer 10
> > # Input PDB name
> > pdb 1HGA-B-K66N-renum.pdb
> > # Output topology name
> > top 1HGA-K66N-solv.prmtop
> > # Output coordinates name
> > crd 1HGA-K66N-solv.inpcrd
> > # Base leap input script
> > #leapin leap.solvate.in
> > leapin 1HGA-B-tleap.in
> > # Additional script for adding ions etc
> > ionsin leap.ions.in
> > # Tolerance (# of waters off from target allowed)
> > tol 2
> > # 0 - Solvatebox
> > mode 1
> > --------------
> >
> > resulting temp.leap.in
> > ---------------
> > source leaprc.protein.ff19SB
> > source leaprc.gaff
> > addAtomTypes {
> > { "M1" "Fe" "sp3" }
> > { "Y1" "N" "sp3" }
> > { "Y2" "N" "sp3" }
> > { "Y3" "N" "sp3" }
> > { "Y4" "N" "sp3" }
> > { "Y5" "N" "sp3" }
> > }
> > HD1 = loadmol2 ../Ferric-1HGA/HD1.mol2
> > HM1 = loadmol2 ../Ferric-1HGA/HM1.mol2
> > FE1 = loadmol2 ../Ferric-1HGA/FE1.mol2
> > loadamberparams ../Ferric-1HGA/HEM.frcmod
> > loadamberparams ../Ferric-1HGA/1HGA_mcpbpy.frcmod
> > mol = loadpdb 1HGA-B-K66N-renum.pdb
> > bond mol.92.NE2 mol.148.FE
> > bond mol.147.NA mol.148.FE
> > bond mol.147.NB mol.148.FE
> > bond mol.147.NC mol.148.FE
> > bond mol.147.ND mol.148.FE
> > bond mol.91.C mol.92.N
> > bond mol.92.C mol.93.N
> > savepdb mol 1HGA-K66N-dry.pdb
> > saveamberparm mol 1HGA-K66N-dry.prmtop 1HGA-K66N-dry.inpcrd
> > source leaprc.water.tip3p
> > solvateoct mol TIP3PBOX 10 0.9
> > addions mol Na+ 2
> > #addions mol Na+ 1
> > remove mol.6451.O
> > saveamberparm mol 1HGA-K66N-solv.prmtop 1HGA-K66N-solv.inpcrd
> > quit
> > ---------------
> >
> > --
> >
> > 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
> >
> >
>
> --
>
> 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 20 2021 - 07:30:02 PDT
