Re: [AMBER] Group defining heavy atoms

From: Alessandro Contini <>
Date: Thu, 22 Jan 2015 10:11:58 +0100

Hi Thomas,
I should have imagined that my reply would have been quite
naive...Concerning group specification I use the following:

input variables...
Backbone restraints
* * M *
ligand restraints

but I imagine that you have tried this also...

Best regards


Il 22/01/2015 09:47, Thomas Exner ha scritto:
> 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
>> _______________________________________________
>> AMBER mailing list

Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
ResearcherID: F-5064-2012
skype alessandrocontini
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Received on Thu Jan 22 2015 - 01:30:05 PST
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