<div dir="ltr">Hi Javaria,<div><br></div><div>As you have probably seen from a number of mails, this list is intended for Gromacs developers to help each other in developing the code. Please move all usage questions to gmx-users.</div><div><br></div><div>The general answer for how to find new parameters is that you'll first have to read the papers for the force field and algorithm to understand it (e.g. HCT Generalized Born) and then either find parameters in the literature of learn how to derive them.</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Mar 31, 2017 at 8:09 AM, Javaria ashraf <span dir="ltr"><<a href="mailto:jia_ashraf@yahoo.com" target="_blank">jia_ashraf@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:16px"><div id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_2603">Hello and greetings</div><div dir="ltr" id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4022">i am simulating my protein in implicit solvent. the protein has ca2+ ion in it. the gbsa.itp file doesn't have parameters for any ion.</div><div id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4082" dir="ltr">how can i add parameters of my ion?</div><div id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4090" dir="ltr">As mentioned in tutorial.....</div><div id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4156" dir="ltr">[ implicit_<span id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4184">genborn</span>_params ]</div><div id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4212" style="font-size:16.6043px;font-family:monospace">;Atomtype sar st pi gbr hct</div><div id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4213" style="font-size:16.6043px;font-family:monospace"><div id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4214" dir="ltr"><br></div></div><div id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4157" dir="ltr">Values in columns 1-3 are not currently used. Column 4 contains the atomic van der Waals radii, which are used in computing the Born radii. <br></div><div id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4238" dir="ltr">the van der Waals radii of ca2+ is 0.231? is it right? or how can i calculate the hct?</div><div id="m_8673855250349071354yui_3_16_0_ym19_1_1490937962977_4320" dir="ltr">thank you<br></div></div></div><br>--<br>
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