Dear sir/madam
I tried using leap to solvate my modified DNA molecule and then
added the Na+ ions to neutralise the charges om the phosphate. Below is the
script that I used.
__leap.in___________________________
loadAmberPrep prepdg1.in
set DGB restype nucleic
loadAmberPrep prepdg2.in
set DGM restype nucleic
loadAmberPrep prepdg3.in
set DGL restype nucleic
loadAmberPrep prepdc1.in
set DCB restype nucleic
loadAmberPrep prepdc2.in
set DCM restype nucleic
loadAmberPrep prepdc3.in
set DCL restype nucleic
x = loadpdb test.pdb
solvateBox x WATBOX216 10.0
addIons x Na+ 0
saveAmberParm x prmtop.wat prmcrd.wat
______________________________________
If I run this script I get some type of an error.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
WAT 4341
)
(no restraints)
____________________________
how do I rectify this
Thanking you
Prem Raj
Below is the output
_________________________________________________________
>tleap
-I: Adding /disk1/people/ny/amber/a6/dat to search path.
-I: Adding /disk1/people/ny/amber/a6/dat/leap/lib to search path.
-I: Adding /disk1/people/ny/amber/a6/dat/leap/cmd to search path.
Welcome to LEaP!
Sourcing leaprc: /disk1/people/ny/amber/a6/dat/leap/cmd/leaprc
Log file: ./leap.log
Loading parameters: ../dat/parm94.dat
Loading library: ../dat/leap/lib/all_nucleic94.lib
Loading library: ../dat/leap/lib/all_amino94.lib
Loading library: ../dat/leap/lib/all_aminoct94.lib
Loading library: ../dat/leap/lib/all_aminont94.lib
Loading library: ../dat/leap/lib/ions94.lib
Loading library: ../dat/leap/lib/water.lib
>source leap.in
----- Source: ./leap.in
----- Source of ./leap.in done
Loading Prep file: ./prepdg1.in
Loading Prep file: ./prepdg2.in
Loading Prep file: ./prepdg3.in
Loading Prep file: ./prepdc1.in
Loading Prep file: ./prepdc2.in
Loading Prep file: ./prepdc3.in
Loading PDB file: ./test.pdb
total atoms in file: 880
Solute vdw bounding box: 54.262 26.750 26.012
Total bounding box for atom centers: 74.262 46.750 46.012
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 77.355 49.640 48.997 angstroms.
Volume: 188141.887 A^3
Total mass 87147.336 amu, Density 0.769 g/cc
Added 4365 residues.
26 Na+ ions required to neutralize.
Adding 26 counter ions to "x" using 1A grid
Grid extends from solute vdw + 1.87 to 7.97
Resolution: 1.00 Angstrom.
grid build: 2 sec
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 19 sec
(Replacing solvent molecule)
Placed Na+ in x at (-1.04, -4.48, -2.12).
(Replacing solvent molecule)
.........
Done adding ions.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
<DGB 1>: C8 C4 N9 C1'
<DGB 1>: C5 N1 C6 O6
<DGB 1>: C6 C2 N1 H1
.....................
<DCL 10028>: N1 N3 C2 O2
<DCL 10028>: C4 H41 N4 H42
<DCL 10028>: N1 C5 C6 H6
<DCL 10028>: C6 C4 C5 H5
<DCL 10028>: N3 C5 C4 N4
total 168 improper torsions applied
168 improper torsions in old prep form
Building H-Bond parameters.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
WAT 4341
)
(no restraints)
___________________________________________________
Thank you in advance
Prem raj
_________________________________________________________________________
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Received on Thu Sep 14 2000 - 22:31:57 PDT
