[Chimera-users] Problem adding charges to RNA
meng at cgl.ucsf.edu
Tue Oct 19 13:41:35 PDT 2010
Please use "Help... Report a Bug" and attach the file, and include a description of any steps needed to reproduce the problem, and your e-mail address if you want to be updated on our conclusions. There is no way to figure out what is happening until we can reproduce the problem. Thanks,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Oct 19, 2010, at 1:36 PM, Andrea L Edwards wrote:
> Yes, the residue names were not being recognized as standard, so I changed the pdb file. Now I can successfully add charges to my RNA. However, now when I go to add them to my ligand (after adding H to the ligand alone), It correctly guesses the net charge. When I click "ok" after it guessed the charge, chimera crashes rather than computing the partial charges. How can I prevent this?
> On Oct 19, 2010, at 2:28 PM, Elaine Meng wrote:
>> Hi Andrea,
>> In general, if there are "nonstandard residues" in your structure, a dialog would appear in which you can specify the net charge of each one (i.e. not the partial charge on each atom, which it will calculate, but the charge of the whole residue). If the guesses in the dialog are correct, you can just go ahead. This dialog appears whether I'm using the command or the Add Charge GUI, so I don't understand what you are saying about there being no way to set their charges. You choose them from pulldowns to the right of each residue name.
>> However, the more fundamental problem in this case is that the residues are not being recognized as standard. If they were recognized as standard RNA residues, you would not get this nonstandard residues dialog, and the atoms would just be assigned charges from a lookup table.
>> Probably your input structure file is not using standard residue and atom names. I suggest using "Help... Report a Bug" in the Chimera menu and attaching your input structure file to the report. It may be, however, that the problem is in the naming in that file (rather than a bug). It may be that you need to edit the file to use standard names before reading it into Chimera. Using Help... Report a Bug will also automatically include information about your system and what version of Chimera you are using, which are generally needed to solve any problem.
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> On Oct 19, 2010, at 12:18 PM, Andrea L Edwards wrote:
>>> When I try to add charge to the RNA molecule, I get a message that says "Please specify the net charges for the above residues so that their atomic partial charges can be computed." And above the message it lists every residue in my molecule. What do I do? I cannot find anyway to specify the net charges, and I though that this script was going to assign the charges anyway, so why do I need to specify them before hand?
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