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 Fri Jun 18 2021 - 02:30:02 PDT
