> 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 - 14:30:07 PDT
