Thanks again everyone.
I will do everything again on Xleap just to be sure.
David
On Thu, Aug 11, 2011 at 4:15 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > I found this on ambermd.org/formats about the prmtop file.
> >
> > %FLAG BOX_DIMENSIONS
> > %FORMAT(5E16.8) OLDBETA, BOX(1), BOX(2), BOX(3)
> > OLDBETA : periodic box, angle between the XY and YZ planes in
> > degrees. This is now redundant, as it is present in the
> > inpcrd files. It is ignored here.
> > BOX : the periodic box lengths in the X, Y, and Z directions.
> > This is now redundant, as it is present in the inpcrd
> files.
> > It is ignored here.
> >
> >
> > Is this current with AmberTools 1.4 and Amber11?
>
> Yes, but this is not sufficient box information for constant pressure
> which requires a count of the number of atoms in each molecule. When you
> re-loaded the PDB, likely this information was not re-created. To do
> this, you need the "set box" command in LEaP (if I remember correctly) or
> to run the solvatebox command again (but with parameters chosen to not
> actually add additional waters). This information includes:
>
> %FLAG SOLVENT_POINTERS
> %FORMAT(3I8)
> 416 37640 355
> %FLAG ATOMS_PER_MOLECULE
> %FORMAT(10I8)
> 1019 1019 1 1 1 1 1 1 1
> 1
> 1 1 1 1 1 1 1 1 1
> 1
> 1 1 1 1 1 1 1 1 1
> 1
>
> Using rdparm, there is a "testwater" command that will tell information
> about the box, waters, etc. If you apply this to the "broken" prmtop, it
> will likely list that it doesn't have the information it needs... Note,
> do not try to use testwater to write a new prmtop since it will be in the
> wrong (archaic) format.
>
> --tec3
>
>
>
>
> rdparm a4t4_RbCl_1M/*topo
>
> \-/
> -/- Welcome to RDPARM (an interactive utility for reading AMBER topology
> files)
> /-\ Type "help" or "?" for more information
> \-/
> -/- Version: "AMBER 11.0 integrated" (4/2010)
> /-\
>
> Residue labels:
>
> DC5 DG DA DA DA DA DT DT DT DT
> DC DG DA DA DA DA DT DT DT DT
> ...
> DC DG3 DC5 DG DA DA DA DA DT DT
> DT DT DC DG DA DA DA DA DT DT
> ...
> DT DT DC DG3 Rb+ Rb+ Rb+ Rb+ Rb+ Rb+
> Rb+ Rb+ Rb+ Rb+ Rb+ Rb+ Rb+ Rb+ Rb+ Rb+
> ...
> Rb+ Rb+ Rb+ Rb+ Rb+ Rb+ Rb+ Cl- Rb+ Cl-
> Rb+ Cl- Rb+ Cl- Rb+ Cl- Rb+ Cl- Rb+ Cl-
> ...
> Rb+ Cl- Rb+ Cl- Rb+ Cl- WAT WAT WAT WAT
> WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
> ...
> WAT WAT WAT WAT WAT WAT WAT
>
> Setting box to be an exact truncated octahedron, angle is 109.471221
>
> RDPARM MENU. Please enter commands. Use "?" or "help"
> for more info. "exit" or "quit" to leave program...
>
>
> RDPARM MENU: testwater
> This parm file appears to have 36131 contiguous waters
> starting at residue 1577, atom 3551
>
>
>
>
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Received on Thu Aug 11 2011 - 14:30:08 PDT
