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<p class="MsoNormal"><span style="font-size:14.0pt"><span lang="EN-US">Dear all,<o:p></o:p></span></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt">After installing cryo_fit in phenix and gromacs_cryofit on my Macbook Pro M1, I now try to test the code using the example data GTPase.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt">The job encounters immediately a problem but the GUI suggests that the job is still running.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt">The log suggest that the first step did not run successfully (below). I presume setting the topology of the protein but I don’t know.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt">Another question is how is it possible to set other parameters for cryo_fit (like ff…) in the GUI or should I run it in command line ?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt">Thank you for your help and suggestions.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt">Philippe.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
<p class="p1"><span class="apple-tab-span"><span lang="EN-US"> </span></span><span lang="EN-US">User's computer's operating system: Darwin<span class="apple-converted-space"> </span><o:p></o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p1"><span lang="EN-US">###############################################################################################<o:p></o:p></span></p>
<p class="p1"><span lang="EN-US">#################### Step 1: Make gro and topology file by regular gromacs ####################<o:p></o:p></span></p>
<p class="p1"><span lang="EN-US">###############################################################################################<o:p></o:p></span></p>
<p class="p1"><span class="apple-tab-span"><span lang="EN-US"> </span></span><span lang="EN-US">Current working directory: /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/CryoFit_1/steps/1_make_gro<o:p></o:p></span></p>
<p class="p1"><span class="apple-tab-span"><span lang="EN-US"> </span></span><span lang="EN-US">command:<span class="apple-converted-space">
</span>python 1_before_pdb2gmx_prepare_pdb.py GTPase_activation_center_tutorial.pdb 0 0 0 True<o:p></o:p></span></p>
<p class="p1"><span class="apple-tab-span"><span lang="EN-US"> </span></span><span lang="EN-US">Current working directory: /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/CryoFit_1<o:p></o:p></span></p>
<p class="p1"><span class="apple-tab-span"><span lang="EN-US"> </span>
</span><span lang="EN-US">This pdb file,<span class="apple-converted-space"> </span>
/Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/GTPase_activation_center_tutorial.pdb , has<span class="apple-converted-space">
</span>6489<span class="apple-converted-space"> </span>atoms<o:p></o:p></span></p>
<p class="p1"><span class="apple-tab-span"><span lang="EN-US"> </span></span><span lang="EN-US">Approximately, for this number of atoms, one 3.1 GHz Intel Core i7 took 7 seconds to make a gro file.<o:p></o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p1"><span class="apple-tab-span"><span lang="EN-US"> </span></span><span lang="EN-US">command:<span class="apple-converted-space">
</span>python 2_runme_make_gro.py /Applications/phenix-1.20.1-4487/modules/cryo_fit/ amber03 True True /usr/local/cryo_fit/cryo_fit/bin//<o:p></o:p></span></p>
<p class="p1"><span lang="EN-US" style="background:yellow;mso-highlight:yellow">Step 1 didn't run successfully</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p1"><span lang="EN-US">User's command was<o:p></o:p></span></p>
<p class="p1"><span lang="EN-US">phenix.cryo_fit /Applications/phenix-1.20.1-4487/modules/cryo_fit/tutorial_input_files/.phenix/project_data/run_1.eff<span class="apple-converted-space"> </span><o:p></o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p1"><span lang="EN-US">phenix.cryo_fit alone without any arguments introduces full options.<o:p></o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p1"><span lang="EN-US">If a user sees a message like<o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">"Fatal error:<span class="apple-converted-space"> </span><o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">Atom xx in residue xx xxx was not found in rtp entry xx with xx atoms<span class="apple-converted-space"> </span><o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">while sorting atoms."<o:p></o:p></span></p>
<p class="p2"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">or<span class="apple-converted-space"> </span><o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">"Fatal error:<span class="apple-converted-space"> </span><o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">Residue xxx not found in residue topology database"<o:p></o:p></span></p>
<p class="p2"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">Solution if these residue/atoms are important:<o:p></o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span class="apple-tab-span"><span lang="EN-US">
</span></span><span lang="EN-US">Fix wrong names of atoms/residues. Running real_space_refine via phenix GUI will show which atoms need to be fixed.<o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span class="apple-tab-span"><span lang="EN-US">
</span></span><span lang="EN-US">If gromacs amber03 force field doesn't have parameters for these residue/atoms, you may need to add appropriate parameters.<o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span class="apple-tab-span"><span lang="EN-US">
</span></span><span lang="EN-US">If you added parameters, please email me (doonam.kim@pnnl.gov), I want to recognize your contribution publicly.<o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span class="apple-tab-span"><span lang="EN-US">
</span></span><span lang="EN-US">Most MD simulation force fields do not support all kinds of rare residue/atoms.<o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span class="apple-tab-span"><span lang="EN-US">
</span></span><span lang="EN-US">cryo_fit2 is under development to address this issue using phenix.eLBOW<o:p></o:p></span></p>
<p class="p2"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">Solution if these residue/atoms are not important:<o:p></o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span class="apple-tab-span"><span lang="EN-US">
</span></span><span lang="EN-US">Remove these "wrong" atoms/residues from user's input pdb file. Run cryo_fit again.<o:p></o:p></span></p>
<p class="p2"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US">Solution if user's input pdb file is big:<o:p></o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p1"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span class="apple-tab-span"><span lang="EN-US">
</span></span><span lang="EN-US">Probably cryo_fit will change conformation just minimally, I would extract out these "wrong" atoms/residues from user's input pdb file, then add these extracted lines to cryo_fitted file later.<o:p></o:p></span></p>
<p class="p2"><span class="apple-converted-space"><span lang="EN-US"> </span></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="p2"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="p1"><span lang="EN-US">Email phenixbb@phenix-online.org or doonam.kim@pnnl.gov for any feature request/help.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
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