>>> My question is what this (bad) prmtop file will do on the pressure
>>> calculations. In both, (bad) prmtop and (right) prmtop files, I have
>>> exactly the same ATOMS_PER_MOLECULE sections. Does that mean the pressure
>>> calculations will be the same, as well? Or during the pressure
>>> calculations, some other sections in prmtop files (combined with
>>> ATOMS_PER_MOLECULE) are used? Thanks.
>>
>> My guess is that the pressure errors will be completely negligible.
>> Assuming
>> you have lots of water molecules around your biomolecules, the water is the
>> dominant contribution to the pressure. You could do a short re-run of some
>> segment to check this.
>
> Sorry...I think I misread your original questions, and have lost the thread
> of the argument. If the two prmtops have the same ATOMS_PER_MOLECULE
> section,
> then I think the pressures should be the same. But, if the have the same
> ATOMS_PER_MOLECULE section, then ambpdb output should also be the same. So
> I'm kind of lost here. [It's too late at night....]
Dave -
Just to clarify what I did, I created 2 prmtop files. In one case (the way my
original prmtop files were created), the AG ions are put at the end of
proteins. Following your notations, it looks as follows:
DNA Strand 1
TER
DNA Strand 2
TER
Protein chain1
TER
Protein chain2
TER
AG1
TER
AG2
TER
END
Bond command was used to connect AG1 with four residues in Protein Chain 1, and
AG2 with four residues in Protein Chain 2. This system was then neutralized
with Na+ ions and solvated with WAT molecules. K+ and Cl- were included later
to make it look like in "physiological conditions". prmtop1/inpcrd1 were
created at the end.
The second prmtop was created for the same system (with modified AG position in
the .pdb file) with the following sequence:
DNA Strand 1
TER
DNA Strand 2
TER
Protein chain1
TER
AG1
TER
Protein chain2
TER
AG2
TER
END
Again, bond command was used to connect AG1 with four residues in Protein Chain
1, and AG2 with four residues in Protein Chain 2. Again, the system was
solvated with Na+, K+, Cl-, and Water the same way as before. Prmtop2/inpcrd2
were created at the end.
When I look at the ATOMS_PER_MOLECULE sections of both prmtop files, I see the
following (these sections are identical, but here is the first few lines):
------------- ATOMS_PER_MOLECULE sections in prmtop1 and prmtop2 -------------
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8)
725 731 2057 2057 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 1 1 1 1 1 1 1
1
.
.
.
-------------------------------------------------------------------------------
DNA Strand 1 and 2 have 725 and 731 atoms, respectively, while the identical
protein chains have 2056 atoms. So, leap added each AG ions to each protein to
define each of them as one molecule (with 2057 atoms) because of the 'bond'
command used in leap.
Everything up to here is right; right number of atoms were defined in
ATOMS_PER_MOLECULE section. I realized the issue when I tried to create the
.pdb files for prmtop1, but if this is the only issue (.pdb creation using
ambpdb) I am ok with that. The sequences in each .pdb file (which were used to
create the prmtop files) are different, and if ambpdb uses ATOMS_PER_MOLECULE
section in creating .pdb file for a given coordinate file, TER cards will be
misplaced. This was the discussion in amber mailing list back in 2005.
My only concern is if the first prmtop1 will affect the MD simulations. If
nothing else in the prmtop files (other than ATOMS_PER_MOLECULE section) is
used in pressure calculations, both prmtop1 and prmtop2 will calculate the
pressures right. That is, at least, what I understood from your and Jason's
comments. Thanks.
Best regards,
Ilyas,
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Received on Tue Jul 03 2012 - 13:00:02 PDT
