Well, I wouldn't necessarily call it a bug. I think the confusing thing
is that the command used to be called "closestwaters", I think(?).
Now the the command is officially "closest" (although closestwaters
is still supported). I actually had the same problem as you the first time
I used the command because it seems like using "closestwaters" should
only give you solute and the closest waters. But ptraj isn't smart enough
to know that you don't want ions. We could add a feature to
automagically remove ions but that carries with it it's own set of problems.
I think using the command "closest" helps set expectations for the output
a little better. Perhaps the manual should be updated to remind users to
strip ions if they don't want them.
--Niel
________________________________________
From: Bruno Rodrigues [bbrodrigues.gmail.com]
Sent: Friday, August 05, 2011 6:53 AM
To: AMBER Mailing List
Subject: Re: [AMBER] 1st shell WITH solvent in ptraj
Well, yeap. It worked pefectly with strip.
But I was trying to wonder what is going on behind the scenes, provided it
should not be the expected behavior.
Do the developers have an idea about this bug?
If you want to take a deeper look on it, I can provide the prmtop and
trajectory files (just one frame, to make it smaller) and you can try to
reproduce the error.
thank you!
On Thu, Aug 4, 2011 at 8:39 PM, Niel Henriksen <niel.henriksen.utah.edu>wrote:
> Try the "strip" command. Strip out the ions and then do
> your "closest" command.
>
> --Niel
> ________________________________________
> From: Bruno Rodrigues [bbrodrigues.gmail.com]
> Sent: Thursday, August 04, 2011 5:02 PM
> To: AMBER Mailing List
> Subject: [AMBER] 1st shell WITH solvent in ptraj
>
> Dear all,
>
> something very strange is happening with a ptraj command I am running.
> Basically, I want to generate a .pdb with the 1st solvation shell with and
> without counterions.
>
> So I made some tests and found out a way to do that. But since I made these
> tests, no matter which script I write, I ALWAYS keep the counterions in my
> .pdb.
>
> for example, the following command:
>
> trajin 1D20_wat_tip4pewmd9_center_short.binpos 6 6 1
>
> solvent byres :39-99999
> closestwater 166 :1-20 first
> trajout 1st_shell.pdb pdb
>
> from 1-20 is my DNA. From 21-38 I have conterions. Then it should count
> only
> the water molecules?
> But it is inserting the ions, no matter their distance, no matter what I
> do.....
>
> the output of the command is enclosed.
>
> Another thing, at some point in the past I also set up
> closestwater 1 :21-38 first
> in the ptraj command, to account for the ions, and I realized that since
> then it keeps getting the ions, no matter this command is present. does it
> make sense? If not, why does it keep the 18 ions (even far from the DNA) on
> my pdb?
>
> thank you in advance
>
>
>
>
>
>
> --
> --
> Bruno Barbosa Rodrigues
> PhD Student - Physics Department
> Universidade Federal de Minas Gerais - UFMG
> Belo Horizonte - Brazil
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Fri Aug 05 2011 - 08:30:02 PDT
