<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Victor,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera will use GAFF types for non-standard residues in all those forcefields, and regular AMBER types for standard residues. There is no option to use GAFF types for all residues.</div><div class=""><br class=""></div><div class="">--Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 8, 2021, at 10:35 AM, Victor Nazarychev <<a href="mailto:nazarychev@imc.macro.ru" class="">nazarychev@imc.macro.ru</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello, Eric,<div class=""><br class="">Sorry for the delay with response. But when I chose the Tools>Amder>Write Prmtop> in the menu Select force field type I only can select 6 force fields, and GAFF could not be chosen. </div><div class=""><br class="">Could you please direct where in the Chimera menu I can select the option to build a GAFF force field using the menu "Write Prmtop"? </div><div class=""><br class="">Best regards, <br class="">Victor<br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">ср, 27 окт. 2021 г. в 20:58, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>>:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;" class="">Hi Victor,<div class=""><span style="white-space:pre-wrap" class=""> </span>I'm not sure I understand the question. The Write Prmtop tool will write a .prmtop file using GAFF types if necessary. That prmtop file uses a somewhat older version of the prmtop format, but most tools will still read it.</div><div class=""><br class=""></div><div class="">--Eric<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Oct 27, 2021, at 2:43 AM, Victor Nazarychev <<a href="mailto:nazarychev@imc.macro.ru" target="_blank" class="">nazarychev@imc.macro.ru</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Dear Eric, <div class=""><br class=""></div><div class="">Thank you for your help. </div><div class=""><br class=""></div><div class="">Maybe you know how to build *.prmtop file of substance namely in the GAFF force field, using Chimera's tools?</div><div class=""><br class=""></div><div class="">Best regards, </div><div class="">Victor </div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">вт, 26 окт. 2021 г. в 20:14, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" target="_blank" class="">pett@cgl.ucsf.edu</a>>:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Victor,<br class="">
Most of Chimera uses AmberTools18 (e.g. minimization; charge addition), but specifically the tools in the Tools→Amber menu use functionality provided by sleap, which is not distributed with current versions of AmberTools. Those tools use AmberTools 1.5, which was released in 2011.<br class="">
<br class="">
--Eric<br class="">
<br class="">
Eric Pettersen<br class="">
UCSF Computer Graphics Lab<br class="">
<br class="">
<br class="">
> On Oct 26, 2021, at 2:21 AM, Victor Nazarychev via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" class="">chimera-users@cgl.ucsf.edu</a>> wrote:<br class="">
> <br class="">
> Dear Chimera's users, <br class="">
> <br class="">
> I built amber's .inpcrd and prmtop files using command write prmtop from Tools/Amber/Write Prmtop. I used Chimera 1.15 (build 42334), but how could I figure out what version of AmberTools is incorporated in this Chimera release? <br class="">
> <br class="">
> Best regards, <br class="">
> Victor<br class="">
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