Hi George, It seems wrong if you see the ions and you save the data to a file, but then that data file doesn’t have the ions. You can check net charge by running addcharge again after reopening that data. You could try submitting a bug report from the Help menu but you’d need to attach a session with the solvent and ions in it from which your saving didn’t include the ions. However, it might not be a bug of Chimera itself since it sounds like all the steps used Ambertools. Elaine
On Aug 8, 2017, at 1:19 PM, George Tzotzos <gtzotzos@me.com> wrote:
Hi Elaine,
In answer to your questions (a) I saved the complex_solv files from the data shown in the image; (b) I opened the files in Chimera. No ions were included.
Best regards
George
On 8 Aug 2017, at 22:02, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi George, I can’t tell what the charges are or whether it is neutral without having some data files. If you chose the option to neutralize I would guess the system is neutral. In the image you sent, it looks like you already have several ions and the water box. Did you really want to add more solvent after that? Are you saying you saved complex_solv files from the data shown in the image? Is the question why these files don’t have ions? The ions are shown in the image. I don’t know anything about cpptraj or whether it is correct that the complex_solv files don’t have ions. I would open those files in Chimera to see if the ions were included. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 8, 2017, at 11:37 AM, George Tzotzos <gtzotzos@me.com> wrote:
In MD movie I loaded complex.prmtop and complex.inpcrd files
In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I’m attaching a snapshot showing the Na+ ions in red).
I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 NOTE: I unticked the Removed existing ions/solvent box
I obtained the following Warning “Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA
I generated complex_solv.prmtop and complex_solv.inpcrd files
When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below).
resinfo #Res Name First Last Natom #Orig #Mol 1 ASP 1 14 14 1 1 2 THR 15 28 14 2 1 ——————— 250 LEU 3988 4006 19 250 3 251 VAL 4007 4023 17 251 3 252 KBR 4024 4062 39 252 4 253 WAT 4063 4065 3 253 5 ———— 10272 WAT 34084 34086 3 10272 10024 10273 WAT 34087 34089 3 10273 10025
Is this what should be expected? Should I consider the solvated complex charge neutralised?
Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions
Thank you in advance for any suggestions.
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