Why you are doing simulation without chromophore? Chromophore is important in GFP. If you want i can send you the forcefield which i am using for GFP. <br>Rama<br><br><div class="gmail_quote">On Wed, Jun 22, 2011 at 10:29 PM, bharat gupta <span dir="ltr"><<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi Sir,<div><br></div><div>Actually I am doing the simulation without the chromophore. So, planarity does not matter to be .. <br>
<div><br></div><div><div><div></div><div class="h5"><br><br><div class="gmail_quote">On Thu, Jun 23, 2011 at 2:23 PM, Ramachandran G <span dir="ltr"><<a href="mailto:gtrama@gmail.com" target="_blank">gtrama@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi Bharat,<br> I used Amber force field, but still i am not statisfied with the parameters which i used because after some nanosecond simulation(1 -2 ns)<br>
the planarity of the sturcture changes. I tired changing the force constant but still not much successfull. If you got success please let me know.<br>
<br>with regards,<br>Rama<br><br><div class="gmail_quote"><div>On Wed, Jun 22, 2011 at 10:11 PM, bharat gupta <span dir="ltr"><<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>></span> wrote:<br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<div><br></div><div><div>I want to simulate a docked complex of my protein (GFP) with phosphotyrosine. I have found this - ffG43a1p forcefield contains parameters for pTYR, so I want to know how good is this FF for simulating my system... As in the literature its mentioned that people have used CHARMM, AMBER, OPLS ff for simulation of GFP. So, using this will be a correct choice or not ...<br clear="all">
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