to follow up on Tom's last sentence ("make it so all the molecules are
together in the prmtop"), here is a bit of info on how to do it:
Modify the pointers in your prmtop so that all the solute molecules are in 1
"molecule"
- here is a sample prmtop for a dimer- the goal is to put both monomers
into a single "molecule"
%FLAG SOLVENT_POINTERS
%FORMAT(3I8)
830 10924 3
-
- this data is really in this format
FORMAT(12I6) IPTRES, NSPM, NSPSOL
IPTRES : final residue that is considered part of the solute,
reset in sander and gibbs
NSPM : total number of molecules
NSPSOL : the first solvent "molecule"
-
- what you need to do is to
- leave IPTRES alone (your solute is not changing)
- change NSPM to match your "new" # molecules (if you make a dimer
into a single molecule, subtract 1. if you make 3 molecules
into 1, subtract
2).
- change NSPSOL the same way- subtract 1 or 2 or more, depending on
what you subtracted from NSPM
- here is the "new" SOLVENT_POINTERS section that turns the 2 monomers
in a single molecule:
%FLAG SOLVENT_POINTERS
%FORMAT(3I8)
830 10923 2
- now for the next section to change- atoms per molecule.
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8)
6015 6015 3 3 3 3 3 3 3 3
3 3 3 3 3 3 3 3 3 3
-
- what you want to do is combine the first two "molecules" (the
monomers) into a single molecule.
- change the "atoms per molecule" to combine the atoms from the two
molecules
- in this case, 6015+6015=12030
- move the numbers up- in this case, change the second 6015 to a 3,
and delete the last 3 at the end of this section.
- here is the modified section (not showing the removal of the final 3
from the end of this section- bu make sure you delete it).
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8)
12030 3 3 3 3 3 3 3 3 3
3 3 3 3 3 3 3 3 3 3
- *SAVE THIS TO A NEW FILE NAME, MAKING IT CLEAR BY THE NAME THAT YOU
MODIFIED THE MOLECULE POINTERS*
On Tue, Sep 27, 2011 at 4:55 PM, Thomas Cheatham III <tec3.utah.edu> wrote:
>
> > I try to resend my email that probably was not read/received.
> > Any hint to fix my RMSD values would be really appreciated.
>
> There is probably not an easy way to fix. Look through the archive as
> suggested about imaging issues and try things like center only the first
> residue of each chain, etc. and imaging. Imaging based on the first atom
> rather than center of mas, etc.
>
> This was what prompted the question on the reflector back to you about box
> size / amount of solvent. Likely there is too little, so there is not an
> easy way to, by generic procedure, image the molecules back since the
> periodic image may be closer than the unit cell, i.e. once it is wrapped,
> it becomes closer to its image.
>
> I have been meaning to write a smarter imaging routine that would attempt
> to minimize distances, however I have not done this.
>
> There are ways to make it so all the molecules are together in the prmtop
> which will prevent this.
>
>
> --tec3
>
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Received on Tue Sep 27 2011 - 14:30:03 PDT
