Hi all,
thank you dan, that was my way of doing it as well.
I recieved a number of replies outside the board. Apparently the most
commonly used way ist to extract the pdb files with ptraj and then load
them into schrodingers maestro and superimpose them there, save and
merge the pdbs into a mdcrd file again. So there appears to be a need
for this functionality.
regards,
simon
On 01/23/2012 05:02 PM, Daniel Roe wrote:
> Hi,
>
> Centering/imaging followed by an RMS fit is definitely the way to go.
>
> On Mon, Jan 23, 2012 at 9:05 AM, Simon Becker
> <simon.becker.uni-konstanz.de> wrote:
>> side of the other one. So far my experiments with the center and image
>> keywords were unsuccessful.
> Imaging with multiple molecules can definitely be challenging. A
> general strategy that works for me is to do one round of
> imaging/centering for each molecule I have, each time adding one more
> molecule to the mask. For example, for 2-stranded DNA where each
> strand is considered a separate molecule I use:
>
> # Strand 1
> center :1-30 origin mass
> image center origin
> # Strand 1 + Strand 2
> center :1-60 origin mass
> image center origin
>
> If you post some more details about your system (# of molecules etc)
> along with the commands you have already tried, we may be able to give
> you more detailed advice.
>
> -Dan
>
>> Regards,
>> Simon
>>
>> --
>> Simon Becker
>> Dept. of Biology
>> Molecular Bioinformatics
>> Box M647 Universitaet Konstanz
>> D-78457 Konstanz
>> mail: simon.becker.uni-konstanz.de
>> Tel: 0049 7531 882900, Fax: 3183
>>
>> http://strucbio.biologie.uni-konstanz.de/
>>
>>
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>
>
--
Simon Becker
Dept. of Biology
Molecular Bioinformatics
Box M647 Universitaet Konstanz
D-78457 Konstanz
mail: simon.becker.uni-konstanz.de
Tel: 0049 7531 882900, Fax: 3183
http://strucbio.biologie.uni-konstanz.de/
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Received on Tue Jan 24 2012 - 00:00:02 PST
