Input from Avogadro, solvation.
Dear Chimera, Three basic questions: I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as or that the atom is not “listed” . Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ? 2) If I use Tools to solvate a model, should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions. 3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory ? Regards, Paul Buscemi, UMN BICB
Dear Chimera, This is the other common error which strangely appears to occur on my PC much more frequently than on my iMac – using the same mol2 file From: Paul Buscemi [mailto:busce004@umn.edu] Sent: Saturday, May 20, 2017 5:02 PM To: chimera-users@cgl.ucsf.edu BB Subject: Input from Avogadro, solvation. Dear Chimera, Three basic questions: I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as or that the atom is not “listed” . Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ? 2) If I use Tools to solvate a model, should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions. 3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory ? Regards, Paul Buscemi, UMN BICB
I found that the daily update 2017 05 16 could not open Avogadro files, but that stable version 1.11.2 could. Hope this helps you. Paul From: P. Buscemi [mailto:busce004@umn.edu] Sent: Saturday, May 20, 2017 5:20 PM To: 'BB' Subject: FW: Input from Avogadro, solvation. Dear Chimera, This is the other common error which strangely appears to occur on my PC much more frequently than on my iMac – using the same mol2 file From: Paul Buscemi [mailto:busce004@umn.edu] Sent: Saturday, May 20, 2017 5:02 PM To: chimera-users@cgl.ucsf.edu BB Subject: Input from Avogadro, solvation. Dear Chimera, Three basic questions: I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as or that the atom is not “listed” . Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ? 2) If I use Tools to solvate a model, should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions. 3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory ? Regards, Paul Buscemi, UMN BICB
This particular bug was fixed on the 19th — if you get the current daily build you won’t get this “coercing to Unicode” error. —Eric Eric Pettersen UCSF Computer Graphics Lab
On May 20, 2017, at 3:20 PM, P. Buscemi <busce004@umn.edu> wrote:
Dear Chimera,
This is the other common error which strangely appears to occur on my PC much more frequently than on my iMac – using the same mol2 file <image001.png>
From: Paul Buscemi [mailto:busce004@umn.edu] Sent: Saturday, May 20, 2017 5:02 PM To: chimera-users@cgl.ucsf.edu BB Subject: Input from Avogadro, solvation.
Dear Chimera,
Three basic questions:
I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as
<PastedGraphic-1.png>
or that the atom is not “listed” .
Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ?
2) If I use Tools to solvate a model, should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions.
3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory ?
Regards,
Paul Buscemi, UMN BICB _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks for the response, A redownload worked... would you please take a stab at particularly #2 . For # 3 I saw an 2013 blog that multicore was not supported and I take this to still be the case. Regards, Paul
On May 22, 2017, at 4:48 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
This particular bug was fixed on the 19th — if you get the current daily build you won’t get this “coercing to Unicode” error.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
From: Paul Buscemi [mailto:busce004@umn.edu <mailto:busce004@umn.edu>] Sent: Saturday, May 20, 2017 5:02 PM To: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB Subject: Input from Avogadro, solvation.
Dear Chimera,
Three basic questions:
I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as
<PastedGraphic-1.png>
or that the atom is not “listed” .
Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ?
2) If I use Tools > Amber> solvate to solvate a model, should I use the “Start solvate tool” under when starting a MD run ?
3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory or just a great CUDA GPU ?
Regards,
Paul Buscemi, UMN BICB _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi Paul, (1) It is generally impossible to figure out what is going on without having examples of your file(s) and being able to reproduce the problem. I’ve never used Avogadro or files from Avogadro. Make sure the PDB or mol2 file is plain text, but that might not be the problem. You could try using menu: Help… Report a Bug and include a brief description of what you did and attach an example file. (2) You didn’t say, but I’m guessing you are using Minimize Structure and/or Molecular Dynamics. If you already used the Solvate tool, there is no need to click the button on the Molecular Dynamics tool to open the Solvate tool again. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html I don’t know if you want your molecular dynamics calculation to use periodic boundary conditions or not. You need to figure that out and then set the option accordingly. If you do choose that option, you need to have added a solvent box. Others will have to weigh in about your other issues since I don’t know the answers. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 20, 2017, at 3:02 PM, Paul Buscemi <busce004@umn.edu> wrote:
Dear Chimera,
Three basic questions:
I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as
<PastedGraphic-1.png>
or that the atom is not “listed” .
Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ?
2) If I use Tools to solvate a model, should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions.
3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory ?
Regards,
Paul Buscemi, UMN BICB
Thanks you Elaine, This was quite helpful. I read a response from Eric who addressed the first question. It was a bug in a daily build but now fixed. I did re-ask #2 and 3 because I read his response first. Yes I use min and MD and yes, for me the box is a necessity. Best Paul
On May 22, 2017, at 3:54 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Paul, (1) It is generally impossible to figure out what is going on without having examples of your file(s) and being able to reproduce the problem. I’ve never used Avogadro or files from Avogadro. Make sure the PDB or mol2 file is plain text, but that might not be the problem. You could try using menu: Help… Report a Bug and include a brief description of what you did and attach an example file.
(2) You didn’t say, but I’m guessing you are using Minimize Structure and/or Molecular Dynamics. If you already used the Solvate tool, there is no need to click the button on the Molecular Dynamics tool to open the Solvate tool again. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html
I don’t know if you want your molecular dynamics calculation to use periodic boundary conditions or not. You need to figure that out and then set the option accordingly. If you do choose that option, you need to have added a solvent box.
Others will have to weigh in about your other issues since I don’t know the answers. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 20, 2017, at 3:02 PM, Paul Buscemi <busce004@umn.edu> wrote:
Dear Chimera,
Three basic questions:
I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as
<PastedGraphic-1.png>
or that the atom is not “listed” .
Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ?
2) If I use Tools to solvate a model, should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions.
3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory ?
Regards,
Paul Buscemi, UMN BICB
Elaine , If yo do not mind giving me a head start on this, Because I am dealing with polymer conformation adsorbed onto on surfaces from solution and entropy can play a huge roll re solvent displacement. Is there any sort of adjustment / account for entropy in MD ? I know this is asking a lot of the system. I saw the mavConservation - AL2CO program but I do know is this is applicable in this type model.. Best Paul
On May 22, 2017, at 3:54 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Paul, (1) It is generally impossible to figure out what is going on without having examples of your file(s) and being able to reproduce the problem. I’ve never used Avogadro or files from Avogadro. Make sure the PDB or mol2 file is plain text, but that might not be the problem. You could try using menu: Help… Report a Bug and include a brief description of what you did and attach an example file.
(2) You didn’t say, but I’m guessing you are using Minimize Structure and/or Molecular Dynamics. If you already used the Solvate tool, there is no need to click the button on the Molecular Dynamics tool to open the Solvate tool again. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html
I don’t know if you want your molecular dynamics calculation to use periodic boundary conditions or not. You need to figure that out and then set the option accordingly. If you do choose that option, you need to have added a solvent box.
Others will have to weigh in about your other issues since I don’t know the answers. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 20, 2017, at 3:02 PM, Paul Buscemi <busce004@umn.edu> wrote:
Dear Chimera,
Three basic questions:
I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as
<PastedGraphic-1.png>
or that the atom is not “listed” .
Is there a preparation I can use for transfer of models ? Alternatively do you suggest any other program to construct models ?
2) If I use Tools to solvate a model, should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions.
3) Im considering building a multicore system ( two 16 core Xeon’s) as a 64 bit system would Chimera take advantage of the multi-core system ? Would the upgrade funds be better spent on memory ?
Regards,
Paul Buscemi, UMN BICB
Hi Paul, The dynamics may reveal entropic effects (does the water have more freedom to move around in one state relative to another state?) but no, the MD tool does not output some entropy value, nor does it calculate free energies, which include entropy. Some other simulation packages (AMBER etc.) include methods for calculating relative free energies (deltaGs), typically involving very long simulations. The AL2CO entropy is something entirely different. It is a measure of conservation per column in a multiple sequence alignment. I hope this clarifies, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2017, at 6:23 PM, Paul Buscemi <busce004@umn.edu> wrote:
Elaine ,
If yo do not mind giving me a head start on this, Because I am dealing with polymer conformation adsorbed onto on surfaces from solution and entropy can play a huge roll re solvent displacement. Is there any sort of adjustment / account for entropy in MD ? I know this is asking a lot of the system. I saw the mavConservation - AL2CO program but I do know is this is applicable in this type model..
Best Paul
Thank you Elaine, This is quite helpful I was not so concerned with calculating S, or delG, but more along the line of , as you suggested, the effects and this should be revealed in protein folding as well as adsorption. Best Paul
On May 23, 2017, at 11:24 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Paul, The dynamics may reveal entropic effects (does the water have more freedom to move around in one state relative to another state?) but no, the MD tool does not output some entropy value, nor does it calculate free energies, which include entropy. Some other simulation packages (AMBER etc.) include methods for calculating relative free energies (deltaGs), typically involving very long simulations.
The AL2CO entropy is something entirely different. It is a measure of conservation per column in a multiple sequence alignment. I hope this clarifies, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2017, at 6:23 PM, Paul Buscemi <busce004@umn.edu> wrote:
Elaine ,
If yo do not mind giving me a head start on this, Because I am dealing with polymer conformation adsorbed onto on surfaces from solution and entropy can play a huge roll re solvent displacement. Is there any sort of adjustment / account for entropy in MD ? I know this is asking a lot of the system. I saw the mavConservation - AL2CO program but I do know is this is applicable in this type model..
Best Paul
participants (4)
-
Elaine Meng -
Eric Pettersen -
P. Buscemi -
Paul Buscemi