xyzedit option 23 program hangs on "Additional Solvation Parameters :"

[BJWiley233]

While running Poltype2 I am encountering issue at step "Fill a Periodic Boundary Box" with ions to neutralize charge. Command normally has input file for the protein and ions such as xyzedit uncomplexed_comp.xyz_2 -k Ribociclib_Bind_comp_config.key 23 < xyzedit_2.in. The size of the box is not yet determined until after this step in Poltype2.

template for xyzedit_2.in:

1 <#atoms in protein>
<iontype> <#ions>

example (with blank line at end):

1 5278
361 4

However I was getting SIGSEGV: Segmentation fault - invalid memory reference. if the <#atoms in protein> is given on the first line so I tested removing that where xyzedit now seems to like the input:

1
361 4

However it hangs at stdout of:

Additional Solvation Parameters :

     Atom Type                PB Size     CS Size     GK Size

         431             2.5740      2.7580      2.9054
         432             2.9059      2.6020      2.5726
... some more atoms of ligand ...
         401             2.9835      3.3560      2.9616

[jayponder]

Hi Brian, The first line of your xyzedit_2.in file is wrong. For the first line of that file, you are trying to use "1 <#atoms in protein>". If you are trying to specify a range of protein atoms that are at the top of the .xyz file, then it should be "-1 <#atoms in protein>". The "-1" signifies the start of a range, so if your protein is the first 5000 atoms, then you want "-1 5000" which will include the range of atoms 1-5000. If you just put "1 5000" then only the two atoms 1 and 5000 will be included.

If that doesn't fix your issue, then please post the files and I can take a look.

[BJWiley233]

Great! I will give this a try.

[BJWiley233]

So at this step in Poltype2 the complex of protein and small molecule are already soaked with a large amount of water molecules and running xyzedit uncomplexed_comp.xyz_2 -k Ribociclib_Bind_comp_config.key 23 < xyzedit_2.in with following input gives a SIGSEGV: Segmentation fault - invalid memory reference error. I ran with a ton of RAM so that can't be issue.

-1 5278
361 4

[misterbrandonwalker]

Im not sure, when I attempt to reproduce I dont get any error and it works fine. What happens when you try this interactively instead of script?

On Mon, May 30, 2022 at 4:44 PM BJWiley23 @.***> wrote:

So at this step in Poltype2 the complex of protein and small molecule are already soaked with a large amount of water molecules and running xyzedit uncomplexed_comp.xyz_2 -k Ribociclib_Bind_comp_config.key 23 < xyzedit_2.in with following input gives a SIGSEGV: Segmentation fault - invalid memory reference error. I ran with a ton of RAM so that can't be issue.

-1 5278 361 4

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[BJWiley233]

I can only try to add the complex with option 23 interactively and not the ions. Then it prompts for "Enter Periodic Box Dimensions (X,Y,Z) : " and that has to be entered in interactive mode. And then you have to hit enter for refining the box option which is Yes by default. I can run it on my mac with the input above and it starts running but hangs at " Steepest Descent Gradient Optimization : " so I will have to get in touch my IT but not sure why it hangs since I minimized the structure. Let me get a little noisy at my IT department and maybe our allocation is corrupted.

[misterbrandonwalker]

It seems as though we might be conflating many steps together? Option 17, for trimming boxes will ask to Enter Periodic Box Dimensions (X,Y,Z) : . Option 21 for creating a period box will prompt you to refine the box after making it I believe.

On Mon, May 30, 2022 at 7:59 PM BJWiley23 @.***> wrote:

I can only try to add the complex with option 23 interactively and not the ions. Then it prompts for "Enter Periodic Box Dimensions (X,Y,Z) : " and that has to be entered in interactive mode. And then you have to hit enter for refining the box option which is Yes by default.

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[BJWiley233]

So my step fails at this line for option 23 in box setup.

Option 23 in xyzedit for me is:

(23) Create and Fill a Periodic Boundary Box

[BJWiley233]

I am wondering since it is adding 4 atoms of atom type 361 for "Chloride Ion" this might be meant to be option 25 and not option 23?

(25) Place Monoatomic Ions around a Solute

So maybe this should be the line in boxsetup.py#L309 under AddIonToSolventBox()

cmdstr=poltype.xyzeditpath+' '+solutexyzfilename+'_'+str(num)+' '+'-k'+' '+keyfilename+' '+'25'+' '+' < '+inputfile

Well that worked 😄! I knew the input was for neutralizing the molecule in the solvent since we do this for GROMACs as well so option 23 from my xyzedit program sounded very weird :). I downloaded the executables from https://dasher.wustl.edu/tinker/downloads/bin-linux-8.10.2.tar.gz

[misterbrandonwalker]

Ah okay it seems perhaps there was a tinker version change. I am using 8.9.4. My option number is (23) Place Monoatomic Ions around a Solute (not 25). I will check out the new version and see about adjusting required tinker version in poltype.

On Mon, May 30, 2022 at 8:54 PM BJWiley23 @.***> wrote:

I am wondering since it is adding 4 atoms of atom type 361 for "Chloride Ion" this might be mean to be option 25?

(25) Place Monoatomic Ions around a Solute

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Brandon Walker Doctoral Candidate, Biomolecular Engineering Lab - Ren Lab 765-414-7787 | https://misterbrandonwalker.com/ https://misterbrandonwalker.com/ @.*** | 107 W Dean Keeton St, Austin, TX 78712 https://maps.google.com/?q=107+W+Dean+Keeton+St,+Austin,+TX+78712

[BJWiley233]

Oh yea. I guess @jayponder has been making some updates :). We can close this now. Thanks!

[jayponder]

Yes, sorry for the confusion. Adding ions is option 25 in the current Tinker version, not 23. You know, "progress" and all that..

[misterbrandonwalker]

Please try with fresh poltype commit. The xyzedit options should be consistent now.

On Mon, May 30, 2022 at 9:01 PM BJWiley23 @.***> wrote:

Oh yea. I guess @jayponder https://github.com/jayponder has been making some updates :)

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Brandon Walker Doctoral Candidate, Biomolecular Engineering Lab - Ren Lab 765-414-7787 | https://misterbrandonwalker.com/ https://misterbrandonwalker.com/ @.*** | 107 W Dean Keeton St, Austin, TX 78712 https://maps.google.com/?q=107+W+Dean+Keeton+St,+Austin,+TX+78712