Yesterday I posted a message regarding Chimera issuing error messages on trying to open trajectory files.
The error was "TypeError: Attempt to form duplicate covalent bond."
I believe that the problem arises from the fact that in preparing the topology files with ANTECHAMBER (tleap) in AMBER, I generated disulfide bonds. My guess is that the problem lies there. Has anyone observed similar behaviour?
Best regards
George
Hi George, The better approach to report Chimera problems is with Help... Report a bug in the menu, or this web form. http://www.cgl.ucsf.edu/cgi-bin/chimera_bug_report_2.py It will let you attach a file (and include your email address if you want feedback).
In this case the trajectory file would be more useful than the error message. Also, I guess we would need both prmtop and trajectory, and I'm not sure if the approach above would let you attach both, so yet another possibility is to send email to chimera-bugs@cgl.ucsf.edu and attach both those files. Please also mention your Chimera version and what kind of computer you are using (e.g. Windows, Mac ...).
Thanks, 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 Nov 28, 2011, at 2:37 AM, George Tzotzos wrote:
Yesterday I posted a message regarding Chimera issuing error messages on trying to open trajectory files.
The error was "TypeError: Attempt to form duplicate covalent bond."
I believe that the problem arises from the fact that in preparing the topology files with ANTECHAMBER (tleap) in AMBER, I generated disulfide bonds. My guess is that the problem lies there. Has anyone observed similar behaviour?
Best regards
George
Hi Elaine,
Many thanks for this. Unfortunately the files are too big to email them. I'd be grateful if you and/or your colleagues could download them from the following link.
http://dl.dropbox.com/u/50952643/2erb-IND-traj.zip
I'm using Chimera version 1.5.3 (build 33475). My operating system is OSX 1.6.8 on a 2x2.93 GHz 6-Core Intel Xeon machine.
Many thanks in advance for all the help.
George
On Nov 28, 2011, at 6:24 PM, Elaine Meng wrote:
Hi George, The better approach to report Chimera problems is with Help... Report a bug in the menu, or this web form. http://www.cgl.ucsf.edu/cgi-bin/chimera_bug_report_2.py It will let you attach a file (and include your email address if you want feedback).
In this case the trajectory file would be more useful than the error message. Also, I guess we would need both prmtop and trajectory, and I'm not sure if the approach above would let you attach both, so yet another possibility is to send email to chimera-bugs@cgl.ucsf.edu and attach both those files. Please also mention your Chimera version and what kind of computer you are using (e.g. Windows, Mac ...).
Thanks, 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 Nov 28, 2011, at 2:37 AM, George Tzotzos wrote:
Yesterday I posted a message regarding Chimera issuing error messages on trying to open trajectory files.
The error was "TypeError: Attempt to form duplicate covalent bond."
I believe that the problem arises from the fact that in preparing the topology files with ANTECHAMBER (tleap) in AMBER, I generated disulfide bonds. My guess is that the problem lies there. Has anyone observed similar behaviour?
Best regards
George
Hi George, Support for the prmtop format used by AmberTools 1.5 was added since the Chimera 1.5.3 release, therefore you need to download the 1.6 daily build to read your trajectory.
--Eric
P.S. Thanks for making your trajectory available. That made it very easy to determine the problem.
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Nov 28, 2011, at 11:01 AM, George Tzotzos wrote:
Hi Elaine,
Many thanks for this. Unfortunately the files are too big to email them. I'd be grateful if you and/or your colleagues could download them from the following link.
http://dl.dropbox.com/u/50952643/2erb-IND-traj.zip
I'm using Chimera version 1.5.3 (build 33475). My operating system is OSX 1.6.8 on a 2x2.93 GHz 6-Core Intel Xeon machine.
Many thanks in advance for all the help.
George
On Nov 28, 2011, at 6:24 PM, Elaine Meng wrote:
Hi George, The better approach to report Chimera problems is with Help... Report a bug in the menu, or this web form. http://www.cgl.ucsf.edu/cgi-bin/chimera_bug_report_2.py It will let you attach a file (and include your email address if you want feedback).
In this case the trajectory file would be more useful than the error message. Also, I guess we would need both prmtop and trajectory, and I'm not sure if the approach above would let you attach both, so yet another possibility is to send email to chimera-bugs@cgl.ucsf.edu and attach both those files. Please also mention your Chimera version and what kind of computer you are using (e.g. Windows, Mac ...).
Thanks, 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 Nov 28, 2011, at 2:37 AM, George Tzotzos wrote:
Yesterday I posted a message regarding Chimera issuing error messages on trying to open trajectory files.
The error was "TypeError: Attempt to form duplicate covalent bond."
I believe that the problem arises from the fact that in preparing the topology files with ANTECHAMBER (tleap) in AMBER, I generated disulfide bonds. My guess is that the problem lies there. Has anyone observed similar behaviour?
Best regards
George
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi Eric,
Many thanks for the immediate reply. Chimera 1.6 works perfectly well.
Best regards
George
On Nov 28, 2011, at 8:17 PM, Eric Pettersen wrote:
Hi George, Support for the prmtop format used by AmberTools 1.5 was added since the Chimera 1.5.3 release, therefore you need to download the 1.6 daily build to read your trajectory.
--Eric
P.S. Thanks for making your trajectory available. That made it very easy to determine the problem.
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.eduOn Nov 28, 2011, at 11:01 AM, George Tzotzos wrote:
Hi Elaine,
Many thanks for this. Unfortunately the files are too big to email them. I'd be grateful if you and/or your colleagues could download them from the following link.
http://dl.dropbox.com/u/50952643/2erb-IND-traj.zip
I'm using Chimera version 1.5.3 (build 33475). My operating system is OSX 1.6.8 on a 2x2.93 GHz 6-Core Intel Xeon machine.
Many thanks in advance for all the help.
George
On Nov 28, 2011, at 6:24 PM, Elaine Meng wrote:
Hi George, The better approach to report Chimera problems is with Help... Report a bug in the menu, or this web form. http://www.cgl.ucsf.edu/cgi-bin/chimera_bug_report_2.py It will let you attach a file (and include your email address if you want feedback).
In this case the trajectory file would be more useful than the error message. Also, I guess we would need both prmtop and trajectory, and I'm not sure if the approach above would let you attach both, so yet another possibility is to send email to chimera-bugs@cgl.ucsf.edu and attach both those files. Please also mention your Chimera version and what kind of computer you are using (e.g. Windows, Mac ...).
Thanks, 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 Nov 28, 2011, at 2:37 AM, George Tzotzos wrote:
Yesterday I posted a message regarding Chimera issuing error messages on trying to open trajectory files.
The error was "TypeError: Attempt to form duplicate covalent bond."
I believe that the problem arises from the fact that in preparing the topology files with ANTECHAMBER (tleap) in AMBER, I generated disulfide bonds. My guess is that the problem lies there. Has anyone observed similar behaviour?
Best regards
George
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Elaine Meng -
Eric Pettersen -
George Tzotzos