Mark,<br><br>This sounds like I use very small forces but expect reasonable effect. But I've applied different forces with step-by-step increasing of force constants ( from very softest comparable with the thermal motion ( 0.1 kj mol nm-2) to relatively hight (10). As the consequence I've observed effect of application of that harmonic constraints wich I've defined in the r0 and r1 range but in some case ( where forses were were hight I've seen perturbation of my structures) and when constraints were low ( in accordance to my literature) I've not seen desired effect like the selection of the constraints was wrong ( but actually all restraints were applied on the correct possitions). This was seen by measurement of the distances between atom pairs wich were contrained. Eg If I define this distances in the 0.1<Rij<0.4 ( r0=0,1 r1=0,4 for this instance) range the real distance between i and j atoms in the simulated structure was lower or higher of the defined range. <br>
<br>By the way I've found that besides such harmonic restraining also I can apply more rigid holo restraints from specified value. Could you tell me where I could find information of the application of such restraints in the topology of my protein? As I understood this could be done by means of editing of the bond enty in topology but what exactly specified type should I applied on the restried atoms?<br>
<br><br>Thank for help again,<br><br>James<br><br><div class="gmail_quote">22 марта 2012 г. 17:32 пользователь Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> написал:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">If there's a car at the bottom of one valley in the Alps, and you think it should be two valleys over, and you pull it with a trained cat... it's not going to move much. How big an animal you need depends on the geography. There need not even be a reasonable route for you to take, if the target valley is effectively on Mars.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="HOEnZb"><div class="h5"><br>
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