Dear Prof. David A. Case,
Thank you for your help, everything is working now.
Best regards,
Ekaterina Nikitina
On Thu, 22 May 2003 10:16:58 -0700
"David A. Case" <case.scripps.edu> wrote:
>On Tue, 20 May 2003, Nikitina Ekaterina wrote:
>>
>> Dear Prof. James W. Caldwell,
>> Some times ago my group (Institute of Applied Mechanics, Russian
>> Academy of Science) has got licensed copy of Amber 7 from your
>>side.
>> Within the calculations in Amber I was faced with a problem that I
>>can
>> not calculate in MD the protein - ligand complexes in a solvent.
>> Unfortunately I have not found in Amber Manual some clear
>>explanation
>> how to create input file *.prepin with parameters gaff for the
>>ligand
>> component and with parameters ff99 for the protein component of the
>> complex and to calculate both components together as adsorption
>> complex. Using Antechamber I can create *.prepin file for the
>>ligand,
>> and after that to put it to xleap, but how to calculate after that
>>the
>> protein ? ligand complex I do not clearly understand.
>> Would you or your colleagues be so kind to explain me how to solve
>> this problem?
>
>Basically, you are most of the way there. You need to create a pdb
>file
>with an initial model of your complex. Put a "TER" card between the
>protein
>and ligand. Then, load your ligand prepin file, followed by the PDB
>file.
>LEaP should recognize everything in the pdb file (work to fix this if
>it
>doesn't). You can then procede to solvate (or whatever) just as for
>a
>protein by itself.
>
>If this doesn't answer your question, you need to ask a more specific
>one.
>
>..good luck...dac
>
>--
>
>==================================================================
>David A. Case | e-mail: case.scripps.edu
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA | http://www.scripps.edu/case
>==================================================================
>
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Received on Sun May 25 2003 - 11:53:02 PDT
