Dear Amber Users:
I'm now trying to use TIP4P water for BOX,
but there happens some problems.
So please give me some advices.
First, I loaded pdb file, and solvate it.
(using "leaprc.f99")
-------------------------------------------------
>bpti = LoadPdb bpti_h.pdb
Loading PDB file: ./bpti_h.pdb
total atoms in file: 875
>SolvateBox bpti WATBOX216 5
Solute vdw bounding box: 34.013 33.898 34.070
Total bounding box for atom centers: 44.013 43.898 44.070
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 46.743 47.144 46.883 angstroms.
Volume: 103314.010 A^3
Total mass 44745.534 amu, Density 0.719 g/cc
Added 2129 residues.
>SaveAmberParm bpti bpti_tip3.top bpti_tip3.crd
--------------------------------------------------
Then I converted this parm and crd files to PDB file with "ambpdb".
--------------------------------------------------
% ambpdb -pqr -p bpti_tip3.top < bpti_tip3.crd > tmp.pdb
| New format PARM file being parsed.
| Version = 1.000 Date = 06/14/02 Time = 08:53:36
--------------------------------------------------
These steps were successfully done.
Then I restarted Leap, and set parameters.
---------------------------------------------------
>WAT = TP4
>set WAT.1 name "TP4"
>LoadAmberParams frcmod.tip4p
---------------------------------------------------
After this preparation, I loaded pdb file and tryed to save this system,
but there happened some errors.
---------------------------------------------------
>bpti = LoadPdb tmp.pdb
>SaveAmberParm bpti bpti_tip4.top bpti_tip4.crd
Checking Unit.
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 57>.A<O 3> and .R<TP4 57>.A<EPW 4>
.
.
.
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 2185>.A<O 3> and .R<TP4 2185>.A<EPW 4>
-- ignoring the warnings.
Building topology.
Building atom parameters.
For atom: .R<TP4 57>.A<EPW 4> Could not find type: EP
.
.
.
For atom: .R<TP4 2185>.A<EPW 4> Could not find type: EP
Parameter file was not saved.
----------------------------------------------------
So I tryed to load new parameter,
>LoadAmberParams parm99EP.dat
>SaveAmberParm bpti bpti_tip4.top bpti_tip4.crd
then I could save this system.
So my first question is "Do I have to use 'parm99EP.dat' when I use TIP4P
water?"
And if so, "Is the result gotten with this parameter enough correct?"
Additionally, when I opened "bpti_tip4.crd" file, I could't find the box
parameter
line at the bottom of this file.
So I thought I should use "SetBox" command in Leap.
---------------------------------------------------
>SetBox bpti vdw
(using default radius 1.500000 for EPW)
.
.
.
(using default radius 1.500000 for EPW)
Box dimensions: 46.742600 47.144600 46.883600
---------------------------------------------------
This system successfully saved.
Is this way correct?
(There isn't such note in manual.)
-----------------------------
Best Regards!
S. Yamasaki
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Received on Thu Jun 13 2002 - 18:05:48 PDT
