[Chimera-users] Bond-type error

[Laia Ferrer Duran]

Thank you very much!

It has to be the space error you mentioned.
I know for sure that the structure was correct because in class it worked.
And I really changed every thing it could be affectin the structure in
every possible way I read all of the program I found in internet.

Yesterday just to try everything I downloaded the old version and it worked
well!.

Thank you for all, the attention in this program is excellent.

El dt., 15 d’oct. 2019, 6:38, Eric Pettersen <pett at cgl.ucsf.edu> va
escriure:

> Okay, this problem is fixed now and the fix will be in the next daily
> build. It might be a few days before we have a successful daily build
> though because we just changed our server hardware and it might take a day
> or two to straighten out the build process. Either use the workarounds I
> mentioned earlier or look for daily builds dated October 14th or later.
>
> —Eric
>
> On Oct 14, 2019, at 3:45 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> Hi Laia,
> Elaine’s answer is accurate in that you will have to change the atom type
> to get the partial-charge determination to work.  However, looking at the
> error you sent it seems there is another problem:  the subprogram handling
> the charge determination (antechamber, from AmberTools) isn’t handling the
> space in the executable’s path name correctly (i.e. the space between
> ‘Program’ and ‘Files’ in C:/Program Files/Chimera
> 1.14rc/bin/amber18/bin/bondtype).  The simplest fix is to revert to using
> Chimera version 1.13.1 for now.  Another possibility is to move your
> Chimera application to a folder with no spaces in its name or its parent’s
> name (i.e. someplace other than “Program Files” and giving the app a name
> other than “Chimera 1.14rc”.  We are working on a fix for this problem.
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>
> On Oct 14, 2019, at 10:32 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> Hi Laia,
> From looking at the PDB information for 2am9, I see that TES is
> testosterone.
> <https://www.rcsb.org/structure/2AM9>
> <https://www.rcsb.org/ligand/TES>
>
> Notice in the chemical diagram in the link above that this molecule has
> double-bond to oxygen from the 6-membered ring.  However, the carbon-oxygen
> bond in this structure is longer than usual for a double bond, so the
> automatic atom-type recognition in Chimera instead assigns this oxygen as
> the O3 type which becomes hydroxyl OH when hydrogens are added. Then the
> Antechamber AM1-BCC charge calculation fails because it sees an
> inconsistency in the structure.
>
> (I noticed that after hydrogen addition, there were two OH on the
> structure when there should only be one according to the chemical diagram.)
>
> You can do either of these:
>
> (1) delete the extra hydrogen (ctrl-click on it to select, then command
> “delete sel”) and then run charge calculation with Dock Prep again (make
> sure to NOT add hydrogens, i.e. uncheck that option so that the hydrogen
> doesn’t get put on again).  Also make sure to set charge of TES in
> add-charge dialog to 0, not  +1 which is the initial estimate.
> OR
> (2) before adding hydrogens, change atom type of the atom named O3 from
> type O3 to type O2 (I can tell its name by pausing the mouse over it), e.g.
> command
>
> setattr a idatmType O2 :TES at o3
>
> … and then the hydrogens will be added correctly as expected for
> testosterone and the charge calculation will run.
>
> It is sometimes necessary to look into the details of the chemical
> structures you are working with, since automatic procedures cannot handle
> everything.  I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Oct 12, 2019, at 1:41 PM, Laia Ferrer Duran <
> laia.ferrerd at e-campus.uab.cat> wrote:
>
> Hi,
>
> I recently started using chimera for one project from university.
> At first I worked in the university computer that it had the program.
> Today, as I have to work from home I downloaded the latest version of
> chimera in the web page and I tried to do a dock prep in the protein from
> DB 2am9.
>
> With the receptor it worked well, but when I done it with the ligand TES
> it seems to have a problem with the add charges fase.
> I searched first in all you webs and all it seems to say is that the
> molecular structure isn't correct but I really think there isn't a problem
> with the structure because with exactly the same steps it used to work in
> the university computer.
>
> The error says:
> (TES) sh: 1: C:/Program: not found
>
> (TES) /usr/bin/antechamber: Fatal Error!
>
> (TES) Cannot properly run "C:/Program Files/Chimera
> 1.14rc/bin/amber18/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o
> ANTECHAMBER_BOND_TYPE.AC -f ac".
>
> Failure running ANTECHAMBER for residue TES
> Check reply log for details
>
> I don't know if it could be some problem with my program or if I should
> change the configuration of the program or what it is that isn't working.
>
> Thanks in advanced and I look forward you answer.
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