<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 Freia,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>When I upgraded Chimera to use Ambertools17 in October, I changed Add Ions and Add Solvent to account for the fact that the ff14SB leaprc file had moved into that ‘oldff’ folder, but missed the fact that WritePrmtop needed the same thing. I have now corrected that, and a fixed version will be in tomorrow’s daily build (look for a daily build dated Jan 6 or newer). Let me know if you run into any other problems…</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div></div><div><blockquote type="cite" class=""><div class="">On Jan 8, 2018, at 5:51 AM, stu118506 <<a href="mailto:stu118506@mail.uni-kiel.de" class="">stu118506@mail.uni-kiel.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" class=""><div style="font-size: 10pt; font-family: Verdana,Geneva,sans-serif" class=""><p class="">Dear Chimera users,</p><p class="">I'd like to save a prmtop file of my protein after preparation for molecular dynamics simulation.</p><p class="">I tried to do it by using Tools - Amber - write Prmtop .</p><p class="">I get this reply log entry:</p><p style="text-align: justify;" class=""><em class="">command: ['/gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap', '-f', '/scratch/tmpOlw0GO/solvate.cmd']</em><br class=""><em class="">Running sleap command: /gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap -f /scratch/tmpOlw0GO/solvate.cmd</em><br class=""><em class="">(writeprmtop) [gtkleap]$ source leaprc.ff14SB</em></p><p style="text-align: justify;" class=""><em class="">(writeprmtop) Error: can not find file leaprc.ff14SB in all the search path.</em></p><p style="text-align: justify;" class=""><em class="">Failure running sleap</em></p><div style="text-align: justify;" class=""> <br class="webkit-block-placeholder"></div><p style="text-align: justify;" class="">I guess that it should source oldff/leaprc.ff14SB because the file seems to be in the directory oldff. But I don't know if that is right and were I have to change the path.</p><p style="text-align: justify;" class="">Additionally, addions works perfectly although leaprc.ff14SB is also needed. So there the path seems to be set correctly.</p><p style="text-align: justify;" class="">Is there anything I can do about it?</p><div style="text-align: justify;" class=""> <br class="webkit-block-placeholder"></div><p style="text-align: justify;" class="">Thank you</p><p style="text-align: justify;" class="">Freia Krause</p><p style="text-align: justify;" class="">Christian-Albrechts Universität zu Kiel,Germany</p>
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