ok sir..<div><br><br><div class="gmail_quote">On Thu, Jun 23, 2011 at 4:06 PM, Ramachandran G <span dir="ltr"><<a href="mailto:gtrama@gmail.com">gtrama@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi,<br> That is the problem. Yet i do not know whether it is working fine not.....i have been working with that for nearly 9-10months but not satisfied yet.<br>In the following mail i will cut and paste the force field parameters which you can use it with amber. If you have time please go ahead and modify according to your wish. <br>
<br>Regards,<br>Rama<div><div></div><div class="h5"><br> <br><br><div class="gmail_quote">On Wed, Jun 22, 2011 at 11:27 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>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
Dear Sir,<div><br></div><div>It will be of great help to send the force field. actually I want to know whether it was working fine for u or not ?? ... Pls send the file and if it's working fine then I think you can deposit it in User contributions in gromacs repository...<div>
<div></div><div><br>
<br><div class="gmail_quote">On Thu, Jun 23, 2011 at 2:38 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">
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<div><div></div><div><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" target="_blank">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><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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