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Re: Maximum number of atoms
BioStanley #17314 03/03/08 10:46 PM
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Except for FEP simulations and maybe QM/MM, the PSF should remain the same throughout a simulation.

Re: Maximum number of atoms
jmwict13 #17315 03/03/08 11:57 PM
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Thank you for information.
Have a nice day.


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Re: Maximum number of atoms
rmv #17316 03/04/08 12:16 AM
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Rick, thanks for helps all the way.
My FEP project scale is much smaller. In that case, I may just adjust parameters to fine tuning the water number.
But I am wondering if it is a good way to truncate the water segment by:
1/ partition the whole file into pieces,
2/ and truncate the pdb, and then read them in and generate psf.
for 2/, the read sequ seems work well for pdb, but some times not very compatible with .crd. For example, MG, DNA, ATP, etc. Do you have any idea on that?

3/ is there any better way to do this?
Thanks

Thanks.


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Re: Maximum number of atoms
BioStanley #17317 03/04/08 02:42 AM
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The better way is usually to use the appropriate PSF, but I'm afraid I'm still completely mystified as to what it is you're trying to do.

Re: Maximum number of atoms
BioStanley #17318 03/04/08 06:54 AM
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Avoid PDB files as much as you can.
READ SEQUENCE from a coordinate file works for any segment, as long as there is one and one only segment in the coordinate file. For solvent it is often more convenient to use the form READ SEQUENCE TIP3 4111.
I don't really see why you need two PSFs for TMD (although I have no personal experience with TMD). All you need to do is to read in the protein coordinates for the target. If the READ COOR TARGET command does not support a selection it should be possible to have a arbitrary coordinates for the rest of the system. Given the heavily restricted nature of TMD you may not even need (explicit) solvent at all.
Concerning the splitting of PSFs: If you have the PSF for a large system, and want PSFs for subsystems you can use DELETE ATOM SELE ... END as an alternative to re-creating the PSF for the subsystem.
Most of your questions are related to CHARMM stuff at a rather more elementary level than the running of TMD ...


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Maximum number of atoms
BioStanley #17319 03/04/08 09:01 PM
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How large is your overall conformational change? Will your final structure fit within the water box of your starting structure?

One thing I have done to accomplish a similar goal is:
1a) generate protein psf and save psf file (protein.psf)
2a) build the solvent box with the intial structure
3a) delete the solute (i.e. everything that is not solvent)
4a) save the solvent psf and coordinates (solvent.psf, solvent.cor)

1b) read in the protein psf file (read psf card protein.psf)
2b) read in the solvent psf (read psf card append solvent.psf)
3b) read in the protein coordinates (read coor card protein.cor)
4b) read in the solvent coordinates (read coor card append solvent.cor)

If your protein structure change isn't too large, you should be able to fix the protein coordinates and clean up the solvent box with minimization. If your protein changes a lot, then you'll probably need to fix the protein and do some dynamics to clean it up.

If your water box is too small to hold your final conformation, then you should probably build the water box with the bigger conformation, eh?


Does that help?


P.S. -- If you're just doing targeted MD (unless there is another TMD I haven't heard of yet), you'll probably not be biasing the water molecules. Couldn't you just read in the endpoint protein coordinates and setup your biasing commands without any clashing water coordinates interfering? I'm probably just rewording Rick and Lennart's comments here.

Last edited by jmwict13; 03/04/08 10:14 PM.

Joshua Ward Graduate Student Purdue University Department of Medicinal Chemistry and Pharmacology
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