Re: [AMBER] Group defining heavy atoms

From: Thomas Exner <thomas.exner.uni-konstanz.de>
Date: Thu, 22 Jan 2015 09:47:31 +0100

Dear David:

Also many thanks to you for your help. Unfortunately, this also does not
work for me. Perhaps, I should explain my problem in a little bit more
detail. I am trying to use AMBER to optimize a number of side chains
while keeping the rest of the molecule as close to the original
structure as possible. The goal is to use these setup in drug design to
have reasonable input structures for MD simulations, which we can also
use for docking. One the one hand, I need for the MD simulations
reasonable atomic positions for all atoms including the ones, which a
not observable in the X-ray structures. On the other hand, I would like
to have structures for comparison, which show all the specific
interactions with ligands as seen in the experiment. Therefore, I use
the restraintmask for constraining all heavy atoms of the residues fully
available from the X-ray structure and constraints on the backbone or
non at all for the residues only partially available. This works very
nice for small to medium sized protein. However, for some proteins these
mask become very large as you see in the following example:

restraintmask=':3,5-38,40-45,47-57,59-61,63-79,81-91,93-105,108,110-116,118-134,136-178,180-181,183,185-194,196-201,203-224,226-237,239-241,243-259,261-273,275-277,279-298,300-310,313-314,316-348,350-369,371-386,388-393,395-399,401-436,438-462,465-492,494-502,504-515,518,520-521,523-535,537-538,540-542,544-554,556-557,559-561,563-567,569-570,572-581&!.H=,OXT|:1-2,4,39,46,58,62,80,92,106-107,109,117,135,179,182,184,195,202,225,238,242,260,274,278,299,311-312,315,349,370,387,394,400,437,463-464,493,503,516-517,519,522,536,539,543,555,558,562,568,571&@C,CA,N,O',

I do not see any chance to get that down to 256 characters and, thus, I
thought to us the groups specification. Another advantage would be to be
able to give different weights to more and less well defined parts of
the structure. However, I have no clue how to do that in a reasonable
way. In worst case I have to recompile the code.

Best.
Thomas


David A Case schrieb:
> On Wed, Jan 21, 2015, Thomas Exner wrote:
>>
>> Just a short question: Is there an easy way for a group definition of
>> all heavy atoms in a residue?
>
> Can you use atommasks instead of groups?
>
> :67&!.H= (or :67&!.H*) should select all atoms in residue 67 whose names
> do not begin with the letter H. See section 19.1 of the Reference Manual.
>
> Also note that you can use the "ambmask" command to help check or debug
> atom expressions, to make sure that you are choosing exactly the atoms you
> want. (That is, note the use of the word "should" in the previous paragraph.)
>
> ....dac
>
>
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>


-- 
________________________________________________________________________________
PD Dr. Thomas E. Exner
Theoretische Pharmazeutische Chemie & Biophysik
Lehrstuhl Pharmazeutische Chemie
Pharmazeutisches Institut
Eberhard Karls Universität Tübingen
Auf der Morgenstelle 8 (Haus B)
72076 Tübingen
Germany
Tel.:    +49-(0)7071-2976969
Mobil:   +49-(0)171-3807485
Fax:     +49-(0)7071-295637
E-Mail:  Thomas.Exner[at]uni-tuebingen.de
Fachbereich Chemie  und Zukunftskolleg
Universität Konstanz
78457 Konstanz
Germany
Tel.:   +49-(0)7531-882015
Fax:    +49-(0)7531-883587
E-Mail: Thomas.Exner[at]uni-konstanz.de
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Received on Thu Jan 22 2015 - 01:00:03 PST
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