January 2018 - Chimera-users - RBVI Mailing Lists

write prmtop, source leaprc.ff14SB
by stu118506 08 Jan '18

08 Jan '18

Dear Chimera users, I'd like to save a prmtop file of my protein after preparation for molecular dynamics simulation. I tried to do it by using Tools - Amber - write Prmtop . I get this reply log entry: _command: ['/gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap', '-f', '/scratch/tmpOlw0GO/solvate.cmd']_ _Running sleap command: /gpfs/fs5/home-sh/sumbi463/.local/UCSF-Chimera64-2017-12-05/bin/amber16/bin/sleap -f /scratch/tmpOlw0GO/solvate.cmd_ _(writeprmtop) [gtkleap]$ source leaprc.ff14SB_ _(writeprmtop) Error: can not find file leaprc.ff14SB in all the search path._ _Failure running sleap_ 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. Additionally, addions works perfectly although leaprc.ff14SB is also needed. So there the path seems to be set correctly. Is there anything I can do about it? Thank you Freia Krause Christian-Albrechts Universität zu Kiel,Germany

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Inquiry about hydrogen bond analysis- important
by Mohamed S. Nafie 08 Jan '18

08 Jan '18

Chimera team. I made the hydrogen bond analysis for the co-crystallized ligand for 1DB1 receptor. it makes on the PDB 6 hydrogen bonds through both oxygen and hydrogen of the hydroxyl group (three of both) with the amino acids residues in the binding site, Also chimera forms 6 but through oxygen of hydroxyl group only. This my first question why? The second question is the structure of the Co crystallized Ligand is not correct, when I adjust the bond order of it by Maestro and save it as pdb and reopen it by Chimera, it forms only two hydrogen binds why? Please try to help me in this question, because I need it necessary Thanks Mohamed S. Nafie Assistant lecturer Chemistry Department, Faculty of Science, Suez Canal University Ismailia, P.O(41522), Egypt Mobile: +201065072524

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regarding opening mouth or poc file on chimera
by Ming 05 Jan '18

05 Jan '18

Hi Chimera team, I have a quick question regarding opening CASTp file on Chimera. I downloaded the pdb file together with mouth and poc file and saved them in the same folder. I also made sure the names are consistent among these files. However, I am still getting error messages as following. Error reading 3mbg.poc: ValueError: Mouth info header missing or IDs not consecutive File "/home/ming/.local/UCSF-Chimera64-1.11.2/share/CASTp/__init__.py", line 88, in processInfoFile " IDs not consecutive" % label.capitalize()) See reply log for Python traceback. I looked up the Chimera manual online and it looks pretty straight forward to open either the mouth or poc file but I am not sure why I keep getting the error messages. Any help will be appreciated. Thanks, Ming

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How to set volume view step size in "vop morph" command
by Zheng Liu 04 Jan '18

04 Jan '18

I want create a morph volume between 2 maps (#0, and #1), as a command I wrote:vop morph #0,1 step 1 playStep 0.04 frames 200 step 1 However, the new model #4 morph was display in step "8", not step "1" in the volume view window. How to set the step size in the vop morph command? Thanks!

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Chimera software error
by محمد عوض على خالد 02 Jan '18

02 Jan '18

Hello everyone. I am interested in using the builtin vina docking tool in Chimera. I get stuck several times at the following Error: ( Running AutoDock Vina for 5x5d failed; see Reply Log for more information: Application stderr ----- 'C:\Program' is not recognized as an internal or external command, operable program or batch file. ----- Application stdout) I check for several tutorials but got the same error, the version I used is Chimera 1.12 and Ulpha version 1.13 in windows 10 platform (64bit) Thank you? Mohammed Khalid Department of Chemistry University of Taif Saudi Arabia ' ________________________________ هذه الرسالة ومرفقاتها (ان وجدت) تمثل وثيقة سرية قد تحتوي على معلومات تتمتع بحماية وحصانة قانونية, ان لم تكن الشخص المعني بهذه الرسالة يجب عليك تنبيه المرسل بخطأ وصولها إليك وحذف الرسالة ومرفقاتها (إن وجدت) من الحاسب الالي الخاص بك ولايجوز لك نسخ هذه الرسالة او مرفقاتها (إن وجدت) أو اي جزء منها أو البوح بمحتوياتها لأي شخص أو استعمالها لأي غرض علما بأن الإفادات والاراء التي تحتويها هذه الرسالة تعبر فقط عن رأي المرسل وليس بالضرورة رأي جامعة الطائف ولا تتحمل جامعة الطائف أي مسئولية عن الأضرار الناتجة عن أي فايروسات قد يحملها هذا البريد . The information in this email and in any files transmitted with it is intended only for the addressee and may contain confidential and/or privileged material. Access to this email by anyone else is unauthorized. If you receive this in error, please contact the sender immediately and delete the material from any computer. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. Statement and opinions expressed in this e-mail are those of the sender, and do not necessarily reflect those of the Taif University. '. If the disclaimer can't be applied, attach the message to a new disclaimer message. ' ________________________________ هذه الرسالة ومرفقاتها (ان وجدت) تمثل وثيقة سرية قد تحتوي على معلومات تتمتع بحماية وحصانة قانونية, ان لم تكن الشخص المعني بهذه الرسالة يجب عليك تنبيه المرسل بخطأ وصولها إليك وحذف الرسالة ومرفقاتها (إن وجدت) من الحاسب الالي الخاص بك ولايجوز لك نسخ هذه الرسالة او مرفقاتها (إن وجدت) أو اي جزء منها أو البوح بمحتوياتها لأي شخص أو استعمالها لأي غرض علما بأن الإفادات والاراء التي تحتويها هذه الرسالة تعبر فقط عن رأي المرسل وليس بالضرورة رأي جامعة الطائف ولا تتحمل جامعة الطائف أي مسئولية عن الأضرار الناتجة عن أي فايروسات قد يحملها هذا البريد . The information in this email and in any files transmitted with it is intended only for the addressee and may contain confidential and/or privileged material. Access to this email by anyone else is unauthorized. If you receive this in error, please contact the sender immediately and delete the material from any computer. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted to be taken in reliance on it, is strictly prohibited. Statement and opinions expressed in this e-mail are those of the sender, and do not necessarily reflect those of the Taif University. '. If the disclaimer can't be applied, attach the message to a new disclaimer message.

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Chimera-users January 2018