<div style="TEXT-ALIGN: left; MARGIN: 0.25in 0in" dir="rtl" class="MsoNormal" align="right"><span dir="ltr"><font size="3" face="Times New Roman">For MD simulation of metalloproteins, people generally change the charge of atoms attached to the metal center based on quantum mechanics studies.</font></span></div>
<div style="TEXT-ALIGN: left; MARGIN: 0.25in 0in" dir="rtl" class="MsoNormal" align="right"><span dir="ltr"></span><span dir="ltr"><font size="3" face="Times New Roman"> If an .itf file shouldn’t be modified, how these changes can be made?</font></span></div>
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<p style="TEXT-ALIGN: left; MARGIN: 0.25in 0in" dir="rtl" class="MsoNormal" align="right"><span dir="ltr"><font size="3" face="Times New Roman">Faezeh</font></span></p></div>
<div class="gmail_quote">On Fri, Jul 22, 2011 at 1:15 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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<div class="im"><br><br>Faezeh Nami wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Dear Itamar<br><br>Thank you for the reply.<br><br>If I modify Cys parameters in the *rtp file in order to add the Cys-label parameters, it will be applied to other Cys in the protein as well. Isn't it?<br>
<br></blockquote><br></div>Set the name of your modified residue to something unique (in both the input coordinate file and the .rtp entry).
<div class="im"><br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">In case of modification of *itp file, should I modify all nr or qtot after the Cys? What about bonds? <br>
</blockquote><br></div>What .itp file do you want to modify? Making changes to the pdb2gmx output is a bad idea. You'll have to change any and all subsequent atom numbers, and that extends to all of the bonded parameters as well, and you will have to add lots in. This procedure is very error-prone. I would suggest building (and thoroughly checking) an .rtp entry for your modified residue.<br>
<br>-Justin<br><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Best,<br>Faezeh
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<div class="h5"><br><br>On Thu, Jul 21, 2011 at 5:51 AM, Itamar Kass <<a href="mailto:itamar.kass@monash.edu" target="_blank">itamar.kass@monash.edu</a> <mailto:<a href="mailto:itamar.kass@monash.edu" target="_blank">itamar.kass@monash.edu</a><u></u>>> wrote:<br>
<br> Hi Faezeh,<br><br> You can modify the FF and add the Cys-label parameters to the *rtp<br> and *hdb files, such that pdb2gmx will be able to use them. Another<br> why is use the original pdb as a starting point and modify the<br>
output *gto, *itp and *top files.<br><br> Just remember that in anycase, it is better to copy the files into<br> your local directory so an change you made will not effect other<br> simulations.<br><br> Cheers,<br>
Itamar<br><br><br> PS I can recommend on this site which can help you in the process<br> <a href="http://compbio.biosci.uq.edu.au/atb/" target="_blank">http://compbio.biosci.uq.edu.<u></u>au/atb/</a><br><br><br> On 21/07/11 7:43 PM, Faezeh Nami wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"> Dear all<br><br> I am trying to simulate a protein which a label (a small organic<br> molecule) is covalently attached to a cysteine. Worth to say there<br>
is no label in the original pdb file of protein and it was<br> attached to the Cys. using a software.<br> Should I insert the label parameters into the conf.gro file or I<br> need to modify a force field? If there is someone who has<br>
experiences in such systems, please have some advice. <br> Thanks in advance,<br> Faezeh <br><br><br><br></blockquote><br> -- <br><br> "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut<br>
<br> ==============================<u></u>=============<br> | Itamar Kass, Ph.D.<br> | Postdoctoral Research Fellow<br> |<br> | Department of Biochemistry and Molecular Biology<br> | Building 77 Clayton Campus<br>
| Wellington Road<br> | Monash University,<br> | Victoria 3800<br> | Australia<br> |<br></div></div> | Tel: <a href="tel:%2B61%203%209902%209376" target="_blank" value="+61399029376">+61 3 9902 9376</a> <tel:%2B61%203%209902%209376><br>
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