Re: [AMBER] Prepping PDB files for amber

From: Lachele Foley (Lists) <"Lachele>
Date: Tue, 20 Dec 2011 15:45:13 -0500

Another site will do more for you, like let you choose HIS protonation
states and set disulfide bonds. It also gives you back Amber
prmtop/inpcrd files and the leap input that was used. You might need
the latter if you want to change the force field, etc. Definitely
download the changed PDB, too, if you want to customize. I think this
one is just ff99, not ff99SB, so you probably want to re-run leap. If
you need SCEE and SCNB written, then you must run leap for yourself.

Note that you might have to pre-sanitize some PDB files rather
extensively -- like I said, this tool is getting a bit dated. For
example, for PDB ID 1NXC, I had to delete everything except the
protein from the file to get it to work. (See also Dave's email).

Also... there is a bug with adding counter ions (say "cancel" for
now). I'll try to get that fixed. Works sometimes... sometimes not
so much. Heisenbugs are hard to fix, but I'll see what I can do.

This still doesn't automate you. Gonna go now to see how much of a
pain it will be to share, but don't get your hopes up. The code might
not be easy to extract out for someone.

There are some tools that might help if you're likely to write code.
If you like python, MMTK would probably be useful. I'm sure there are
others. If you're more comfy with C, Glylib has some utils that might
help (or make you scream in terror, depending on your point of view). -- very rough in many ways, but occasionally
useful. We're working on a better version of that, too, but it might
be a little while.

On Tue, Dec 20, 2011 at 2:58 AM, Jan-Philip Gehrcke
<> wrote:
> On 20.12.2011 01:56, Thomas Gaillard wrote:
>> Le Tuesday 20 December 2011 à 12:18:51AM, Jan-Philip Gehrcke a écrit :
>>> 2) Verify disulfide bonds with literature
>>> =========================================
>>> 12 bridges to 108
>>> 62 bridges to 114
>> You can also read which CYS are engaged in a disulfide bond from the PDB
>> headers (SSBOND entries) and rename them to CYX automatically.
>> $ grep SSBOND 3EAC.pdb
>> SSBOND   1 CYS A  122    CYS A  164                          1555   1555  2.03
>> ...
> Would you in any case rely on the PDB header? :)
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Tue Dec 20 2011 - 13:00:04 PST
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