[AMBER] I do need your help, please

From: William Flak <williamflak.yahoo.com>
Date: Thu, 8 Apr 2010 12:04:50 -0700 (PDT)

Dear AMBERI know my questions may look silly, but I got confused, I did read lot of papers, emails and couldn't get a definite answer.PLEASE, I do need your help.1- Is extra point massless? The original paper says its mass is  3.00 and most of mail on amber list says it is massless.2- what is the difference between massless dummy atom and massless extra point in amber force field?3- why extra point has NONB EP       1.0       0.0? I see in some files, EP NONB values are 0.0 0.0 so which one is the correct value?4- the distance between lone pair and Oxygen (for example) is 0.35. This is the distance between center of oxygen and center of lone pair, The problem is the VWD radius of oxygen is 1.52, does it mean it looks like a loop inside a sphere? so the dominant interaction should be with the oxygen. Sorry for any inconvenience caused by my email.Any kind of help would be appreciated.thanks in advance
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Received on Thu Apr 08 2010 - 12:30:06 PDT
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