Adding bridged water interaction in constraint file

[Anonymous]

Hi,

 

I am working on Rosetta Enzyme Design Application trying to design a protein with a particular ligand in desired geometry. I wanted to define a bridged hydrogen bond interaction between the carboxylate group on the ligand and the arginine residue in protein via water molecule.

I thought of adding two separate constraint blocks in the constraint file: one representing interaction of ligand with water and the other representing interaction of water with arginine. I am using two ligands in my design (ligand and water). I tried to do something similar to the way metal ion interactions are defined but I cannot find the residue name or code or abbreviation to use in the constraint block ATOM_MAP row. (TEMPLATE:: ATOM_MAP: 2 residue1: ??????? )

Also, if there is another way to approach the problem, any suggestions would be appreciated.

Thank you in advance !

 

Greetings,

Purvi

[Anonymous]

Hi Purvi,

I have used constraints with up to three ligands, including a water. I am a little unclear what you are attempting exactly, but there is one key issue with using a discreet water molecule in enzyme design – you can not constrain to the hydrogens in water. The constraints in the constraint block must be between heavy atoms for enzyme design. My understanding is that the hydrogens are stipped at some point before the constraints are applied and then when the constraints are applied it will cause an an atom/atom type not found. 

TL;DR when using water as a ligand in enzyme design only constrain between the heavy atoms and not hydrogen.

If that isn’t your issue, post again and I will see if I can help.

 

Terry

[Anonymous]

Hi Terry,

 

Thank you for the reply. I knew the constraints can only be applied between heavy atoms and not hydrogen but I did not know how to use water in the constraint block. I tried using hydrogens but it indeed gives the error that you mentioned. Also,I could not find residue name abbreviation for water.

In my system, I want to constraint a hydrogen bond between the carboxylate group on ligand and arginine via water. I understand your point of using only heavy atoms but that still doesn’t solve my problem because if I consider the oxygen of water along with any other residue, it will again give me atom/atom type not found.

Could you tell me how did you use water in the constraints with the other ligands? Or how did you use just water in the constraint block?

 

Greetings,

Purvi

[Anonymous]

Hi Purvi,

I am at work at the moment, but when I get home tonight I will post the exact syntax I used for water. If I remember correctly I was using TRP3 water atom types. 

Terry

[Anonymous]

Hi Terry,

 

Thank you so much. I appreciate the effort.

 

Greetings

Purvi Gupta

[Anonymous]

Hi Purvi,

Sorry this took so long. I ended having to ask an old lab mate because I was having issues accessing my old hardrive.

This is how she is constraining water. She took an H2O molecule and ran mol2params on it and then just used it as another ligand.

1. Here’s the example of header for PDB for my 8th cst which is water cst:

REMARK 666 MATCH TEMPLATE B Z00  1 MATCH MOTIF A GLU 26  8  1

2. Here’s syntax in cst file:

#8 – Water to 26E OE1

CST::BEGIN

  TEMPLATE::   ATOM_MAP: 1 atom_name: O H1 H2

  TEMPLATE::   ATOM_MAP: 1 residue3: Z00

 

  TEMPLATE::   ATOM_MAP: 2 atom_name: OE1 CD CG

  TEMPLATE::   ATOM_MAP: 2 residue3:  GLU

 

  CONSTRAINT:: distanceAB:    2.8  0.5    50   1    3

# CONSTRAINT::    angle_A:  180.0 30.0    50   360. 2

  CONSTRAINT::    angle_B:  103.8 10.0    30   360. 2

# CONSTRAINT::  torsion_A:    0.0  0.0    0    360. 2

# CONSTRAINT:: torsion_AB:    0.0  0.0    0    360. 2

  CONSTRAINT::  torsion_B:  191.8 19.0    30   360. 2

 

Let me know if this helps.

 

Terry

[Anonymous]

Hi Terry,

 

Thank you so much. I used the same method as you mentioned. Used water as a separate ligand, created the .params file and constrained only with the heavy atom. I think it is fine now and also working. However, I am getting a new error now.

Segmentation fault (core dumped). These are the last few lines:

core.io.pose_from_sfr.PoseFromSFRBuilder: ResidueType 240: HIS:CtermProteinFull

core.io.pose_from_sfr.PoseFromSFRBuilder: …new residue is a polymer: 1

core.io.pose_from_sfr.PoseFromSFRBuilder: …old residue is a polymer: 1

core.io.pose_from_sfr.PoseFromSFRBuilder: HIS:CtermProteinFull 240 is appended to chain A

core.conformation.Conformation: CURRENT_FOLD_TREE  EDGE 1 238 -1

core.io.pose_from_sfr.PoseFromSFRBuilder: ResidueType 241: 3KR

core.io.pose_from_sfr.PoseFromSFRBuilder: …new residue is a polymer: 0

core.io.pose_from_sfr.PoseFromSFRBuilder: …old residue is a polymer: 1

core.conformation.Conformation: CURRENT_FOLD_TREE  EDGE 1 238 -1  EDGE 1 239 1

core.io.pose_from_sfr.PoseFromSFRBuilder: ResidueType 242: ZOO

core.io.pose_from_sfr.PoseFromSFRBuilder: …new residue is a polymer: 0

core.io.pose_from_sfr.PoseFromSFRBuilder: …old residue is a polymer: 0

core.conformation.Conformation: CURRENT_FOLD_TREE  EDGE 1 238 -1  EDGE 1 239 1  EDGE 1 240 2

Segmentation fault (core dumped)

I am guessing it doesn’t recognise the chains of the ligands. But I am not sure how to solve that.

Do u have any ideas what it could be?

 

Greetings

Purvi

 

[Anonymous]

That error isn’t one I have seen before. Just a sanity check, you added the added the -extra_res Z00.params into your flags file too?

Terry

[Anonymous]

Hi Terry,

 

Thank you so much for your reply. The constraints for water is working for me now.  I added the water .params file before also but I managed to solve the next error also. Apparently, the .params file created by molfile2params.py didn’t include the ICOORDS as it has no neighbouring atoms. So i made oxygen the root atom while creating the .params file and copied the ICOORD rows from the standard HOH.params file from Rosetta. 

It works now Thanks a lot again

 

Greetings

Purvi

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