Dear amber-community,
I am having problems seting up a protein system in Leap with the command
solvatebox using the
TIP4P water model.
solvatebox myprot TIP4PBOX 10
I am using amber9 and I have already installed all the bug fixes and run the
tests
without any problems.
I have already successfully set up exactly the same system using TIP3PBOX
rather than TIP4PBOX.
The system in question is rather small (100 residues), with no net charge
and no unusual or modified
residues. As I can set up and run the same system using TIP3P water
force-field, I don't think that there
is a problem with the protein system itself.
I also tried simply solvating the system with TP4 molecules as suggested by
Ross Walker in a email
that I found in the mail archives using:
solvatebox myprot TP4 10
and I get a similar set of error messages.
I have pasted below the error messages that I get.
I would be very grateful if somebody could tell me where I am going wrong.
Do I have to manually define extra parameters when using the TIP4P water
model?
with best regards,
jc.
I have done the following in Leap
source leaprc.ff03
myprot = loadpdb myprot.pdb
solvatebox myprot TIP4PBOX 10
At this point I get a large number of messages, so many that I can't see
them all in the terminal.
If I look in the leap.log file it says:
Solute vdw bounding box: 24.959 47.051 28.231
Total bounding box for atom centers: 44.959 67.051 48.231
Solvent unit box: 18.860 18.867 18.860
The number of boxes: x= 3 y= 4 z= 3
Adding box at: x=0 y=0 z=0
Center of solvent box is: 18.860000, 28.300500, 18.860000
Adding box at: x=0 y=0 z=1
Center of solvent box is: 18.860000, 28.300500, 0.000000
Adding box at: x=0 y=0 z=2
Center of solvent box is: 18.860000, 28.300500, -18.860000
Adding box at: x=0 y=1 z=0
Center of solvent box is: 18.860000, 9.433500, 18.860000
and so on....
finishing with
(using default radius 1.500000 for EPW)
(using default radius 1.500000 for EPW)
(using default radius 1.500000 for EPW)
(using default radius 1.500000 for EPW)
(using default radius 1.500000 for EPW)
(using default radius 1.500000 for EPW)
Total vdw box size: 48.094 70.203 51.314 angstroms.
Volume: 173249.890 A^3
Mass > 78982.642 amu, Density > 0.757 g/cc
(type - hence mass - of one or more atoms could not be found)
Added 4015 residues.
when I then type
check myprot
I get lots or warnings such as:
WARNING: There is a bond of 0.150502 angstroms between:
------- .R<WAT 62>.A<EPW 4> and .R<WAT 62>.A<O 1>
WARNING: There is a bond of 0.150213 angstroms between:
------- .R<WAT 63>.A<EPW 4> and .R<WAT 63>.A<O 1>
WARNING: There is a bond of 0.149492 angstroms between:
------- .R<WAT 64>.A<EPW 4> and .R<WAT 64>.A<O 1>
WARNING: There is a bond of 0.149469 angstroms between:
------- .R<WAT 65>.A<EPW 4> and .R<WAT 65>.A<O 1>
WARNING: There is a bond of 0.149549 angstroms between:
------- .R<WAT 66>.A<EPW 4> and .R<WAT 66>.A<O 1>
WARNING: There is a bond of 0.149335 angstroms between:
------- .R<WAT 67>.A<EPW 4> and .R<WAT 67>.A<O 1>
though at the end I get the message 'Unit OK'
If I then try to create the topology and coordinate file, I get similar
warning messsages as above followed by more warning messages saying:
For atom: .R<WAT 62>.A<EPW 4> Could not find type: EP
For atom: .R<WAT 63>.A<EPW 4> Could not find type: EP
For atom: .R<WAT 64>.A<EPW 4> Could not find type: EP
For atom: .R<WAT 65>.A<EPW 4> Could not find type: EP
For atom: .R<WAT 66>.A<EPW 4> Could not find type: EP
For atom: .R<WAT 67>.A<EPW 4> Could not find type: EP
For atom: .R<WAT 68>.A<EPW 4> Could not find type: EP
For atom: .R<WAT 69>.A<EPW 4> Could not find type: EP
For atom: .R<WAT 70>.A<EPW 4> Could not find type: EP
For atom: .R<WAT 71>.A<EPW 4> Could not find type: EP
For atom: .R<WAT 72>.A<EPW 4> Could not find type: EP
.......
Parameter file was not saved.
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Received on Sun Jun 17 2007 - 06:07:06 PDT
