<div dir="ltr">Raphael<div><br></div><div>Hai is correct about Phenix not supporting AmberTools16. I have been testing the code to support it and plan on releasing it in a short time frame. I suggest you install AmberTools15 for use with Phenix or wait until the code is updated.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Jul 12, 2016 at 10:01 AM, Hai Nguyen <span dir="ltr"><<a href="mailto:nhai.qn@gmail.com" target="_blank">nhai.qn@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><span class="">On Tue, Jul 12, 2016 at 12:39 PM, R. Gasper-Schönenbrücher <span dir="ltr"><<a href="mailto:raphael.gasper@bph.rub.de" target="_blank">raphael.gasper@bph.rub.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Hi all,<br>
<br>
I am trying to run amber from phenix with a standard pdb file, no co-factors etc and struggle already at the phenix.AmberPrep script.<br>
For unknown reasons, the .prmtop file stays empty (0 bytes). I have tried to figure out from the amber python scripts, where the problem might be, but didn't find anything obvious (the "self.ns_names" variable stays empty)<br>
<br>
The leap log files states two problems:<br>
1) ......Nonterminal, was not found in name map. (for every single amino acid)<br>
2) FATAL: Atom .R<MET 1>.A<N 1> does not have a type. (for every single atom)<br>
which ends up in:<br>
"Failed to generate parameters<br>
Parameter file was not saved."<br>
<br>
There is no .map2 file generated.<br>
<br>
Phenix version: dev-2463<br>
Amber: Ambertools 16<br>
<br></blockquote><div><br></div></span><div>Hi, </div><div><br></div><div>AmberTools16 has renamed the forcefields (for example, leaprc.ff14SB is renamed to leaprc.protein.ff14SB).</div><div>Please see <a href="http://ambermd.org/doc12/Amber16.pdf" target="_blank">http://ambermd.org/doc12/Amber16.pdf</a> (page 33, Molecular mechanics force fields) for further info.</div><div><br></div><div>It's likely that AmberPrep has not updated yet.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>Hai</div></font></span><span class=""><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Every help is highly appreciated.<br>
Many thanks!<br>
Best,<br>
Raphael<br>
<br>
<br>
-- <br>
Raphael Gasper-Schönenbrücher<br>
Universität Bochum<br>
AG Proteinkristallographie, Lehrstuhl für Biophysik, NDEF 04/316<br>
Universitätsstraße 150<br>
44801 Bochum<br>
Germany<br>
Tel: <a href="tel:%2B49%20%280%29234-32%2027086" value="+492343227086" target="_blank">+49 (0)234-32 27086</a><br>
Fax: <a href="tel:%2B49%20%280%29234-32%2014762" value="+492343214762" target="_blank">+49 (0)234-32 14762</a><br>
<br>
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