Sorry about the "organized" term. I think I may have used the wrong word.
What I meant was, "already processed". But anyway, I was just checking if
there was such a script. Another question. I have noticed that all bridges
( at least the ones I already looked at) have a single water molecule
between residues. Does hbond identify if two residues are bridged by more
than one water molecule, i.e., an interaction of the type "RES1 - WAT - WAT
- RES2" ?
Thank you
2013/7/11 Daniel Roe <daniel.r.roe.gmail.com>
> On Thu, Jul 11, 2013 at 12:04 PM, Fabrício Bracht <fabracht1.gmail.com>
> wrote:
> > that are bridged. For the number of water molecules involved in this link
> > and the identity of them, I have to look at the raw "out" file. Isn't
> there
> > a way to obtain such info in a more organized fashion?
>
> #Frame hb[UU] hb[UV] hb[Bridge]
> hb[ID]
> 1 5 27 3
> 208(10+11+),494(2+3+),1409(3+5+),
>
> I feel like this format is pretty organized, considering that every
> frame you can have a different number of solvent molecules bridging 2
> or more solute residues. This line tells me I have 3 bridging solvent
> molecules: solvent residue 208 bridging solute residues 10 and 11,
> solvent residue 494 bridging residues 2 and 3, etc. The information is
> contained in a single string that is readily parsable by your favorite
> text manipulation language so you can organize it into any format you
> prefer (I would probably just use awk).
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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Received on Thu Jul 11 2013 - 16:30:03 PDT
