From owner-chemistry@ccl.net Sat May 24 10:05:00 2014 From: "Julio Dominguez acheron24(a)hotmail.com" To: CCL Subject: CCL: Structure minimization Message-Id: <-50116-140524004852-16814-HZHMHsY6NHAH+/AI/td7DQ%x%server.ccl.net> X-Original-From: Julio Dominguez Content-Type: multipart/alternative; boundary="_8cb65e9e-df0c-4024-80af-ed2680a654ed_" Date: Sat, 24 May 2014 04:48:47 +0000 MIME-Version: 1.0 Sent to CCL by: Julio Dominguez [acheron24() hotmail.com] --_8cb65e9e-df0c-4024-80af-ed2680a654ed_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I wrote a blog post with some simplistic comparisons for "energy minimizati= on": http://macosxpostdoc.blogspot.mx/2011/05/brief-primer-in-energy-minimizatio= n-or.html So=2C what I would recommend you do is to find a metric you can follow=2C f= or example side chain clashes. Then=2C minimize you protein for 10=2C 100 a= nd then 1000 steps of SD.With your metric you can check what was "better"= =2C 10=2C 100 or 1000. Same for CG.=20 I haven't done minimization after Modeller in a long time but I'll would us= e my own advice if I had to. Best regards >=20 = --_8cb65e9e-df0c-4024-80af-ed2680a654ed_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
I wrote a blog post with some simplistic comparisons for "en= ergy minimization":

http://ma= cosxpostdoc.blogspot.mx/2011/05/brief-primer-in-energy-minimization-or.html=

So=2C what I would recommend you do is to fin= d a metric you can follow=2C for example side chain clashes. Then=2C minimi= ze you protein for 10=2C 100 and then 1000 steps of SD.
With your= metric you can check what was "better"=2C 10=2C 100 or 1000. Same for CG.&= nbsp=3B

I haven't done minimization after Modeller= in a long time but I'll would use my own advice if I had to.
Best regards

>=3B
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