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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 17 2021 - 10:30:02 PDT
