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#273 - 06/02/08 12:31 PM Re: hbonds.inp [Re: lennart]
beginner Offline
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Registered: 07/19/04
Posts: 165
perhaps it is a naive question.
Quote:

It is typically not necessary to define a cutoff for the angle.




Since there are many difference criteria have been used in the lipid simulation, is this criteria is also reasonable for the lipid system. I am not so sure becuse we are here mainly focused on the peptide/protein systems.
thank you very much

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#274 - 06/02/08 01:07 PM Re: hbonds.inp [Re: beginner]
rmv Online   content

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The forces between atoms are computed in CHARMM w/o regard to the molecule type; for H-bonds, the partial charges and VDW radii play a major role, esp. in the close approach distance.

If you are comparing to another simulation result, you should probably try to use the same distance and angle criteria.

Otherwise, I suggest trying the COOR HBOND defaults; we've done that in a publication to evaluate lipid:water and lipid:sugar H-bonds.

Making sure you've properly accounted for image interactions may be a more important issue, esp. if the peptide reaches the edge of the simulation cell during the simulation.

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#275 - 10/08/08 08:28 PM Re: hbonds.inp [Re: rmv]
diwakar Offline
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Registered: 03/07/07
Posts: 23
Loc: Cambridge MA
Hi,
I used the code listed here for estimating the number of hydrogen bonds and lifetime. I am wondering is there any way to get the average distance between the donors and acceptors as well ?

Thanks a lot
Diwakar

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#276 - 10/09/08 02:07 AM Re: hbonds.inp [Re: diwakar]
lennart Online   content

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As of CHARMM version 32 the COOR HBONd command can also give the distance distribution, from which you should easily be able to compute the average. From corman.doc:
"Distance and lifetime histograms can be computed for all (putative) hydrogen
bonds encountered in the analysis"
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#277 - 10/13/08 10:00 PM Re: hbonds.inp [Re: lennart]
diwakar Offline
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Registered: 03/07/07
Posts: 23
Loc: Cambridge MA
Thanks a lot for the help.
I have a couple more questions about calculating the number and lifetime of hydrogen bonds.
1) Is it possible to exclude the intra-molecular hbonds?
I calculated the hbonds by selecting each molecule separately and then counting the hbonds of this molecule with other molecule. This process excludes the intra-molecular bonds but I was wondering if there is a better way of doing it.

2) How can I get the number of hbonds as a function of time?

Regards,
Diwakar

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#278 - 10/14/08 01:12 AM Re: hbonds.inp [Re: diwakar]
lennart Online   content

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1/ You did the right thing, there is no other way to do it. Using the two selections is not all that difficult, is it?
2/ Use a COOR HBOND (without keyword VERBose) in a CHARMM loop and write the number of hydrogen bonds (available as a CHARMM substitution variable, see subst.doc) to a file.
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#279 - 11/14/08 06:41 PM Re: hbonds.inp [Re: lennart]
diwakar Offline
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Registered: 03/07/07
Posts: 23
Loc: Cambridge MA
I am trying to get water water hydrogen bonds. I have added the donor list to TIP3 water model as described in the hbonds.inp. I get the same psf without any extra donors on regenerating the psf using this code:

read rtf card name top_all27.rtf
read para card name par_all27.prm

read psf card name @pdbfile@qual.psf
read coor card name @pdbfile@qual.crd

write psf card name @pdbfile@qual-water-donor.psf
write coor card name @pdbfile@qual-water-donor.crd

I want to know if anything more needs to be done to regenrate the psf?

Thanks
Diwakar

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#280 - 11/14/08 07:20 PM Re: hbonds.inp [Re: diwakar]
rmv Online   content

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Yes, you must use the GENERATE command instead of READ PSF

An alternative is the DONOR and ACCEPTOR commands; they seem to work as long as there only one of each in a given CHARMM input.

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#281 - 11/15/08 03:56 AM Re: hbonds.inp [Re: rmv]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
DONOr/ACCEptor ADD have some issues, and do not work properly in older versions of CHARMM. It is really very easy to regenerate the PSF so I strongly recommend that route; if your water segment is the last one all it takes is:
read rtf card name ... ! the new RTF w/ DONO, ACCE for TIP3
read param card name ..
read psf card name old.psf
delet atom sele segid wat
read seque tip3 345
gene wat noangle nodihe
write psf card name new.psf
* PSF for ... with DONO/ACCE for TIP3
*

If water residue numbering in the original PSF was not sequential one may change it to sequential with the JOIN command (struct.doc).
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#282 - 11/15/08 11:53 AM Re: hbonds.inp [Re: lennart]
rmv Online   content

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Registered: 09/17/03
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Loc: 39 03 48 N, 77 06 54 W
A good point; you don't have to start over from the beginning of your model building. What's most important is that the number and ordering of atom types in the PSF does not change. Reading the old PSF and deleting the water segment alone won't work if additional segments were added after the water, such as ions. In that case, you'd need to also delete the segments that follow the water segment in the PSF, and then add them back via GENERATE, in the same order as was done initially.

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