AMBER Archive (2007)

Subject: Re: AMBER: problems using TIP4PBOX

From: Andy Purkiss-Trew (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Wed Jun 13 2007 - 07:36:14 CDT

You need a line such as

frcmodtip4p = loadamberparams frcmod.tip4p

to load the modifications to the forcefield for the extra point (EPW)
that is present in tip4p waters.

If you add this line before the solvatebox command, you shouldn't have
any errors.

Hope this helps

On Wed, 2007-06-13 at 12:53 +0200, john chen wrote:
> 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.
>
>
>
>
>
> 

-- 
Cat, n.: Lapwarmer with built-in buzzer.
+----------------------------------------------------------------------+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
|           E-mail   a.purkiss_at_mail.cryst.bbk.ac.uk                    |
+----------------------------------------------------------------------+

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