[Chimera-users] Problem with added ions in Amber

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 8 13:36:52 PDT 2017


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 at 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 at 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 at 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.
>>> 
>>> <PastedGraphic-1.png>
>> 
> 
> 
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