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[modeller_usage] restraints problem, core dumped



Hi,
I am trying to model a protein with a restrain file

MODELLER6v2 VERSION: USER FORMAT
R 3 1 1 21 2 2 0 7.1000 0.3387 SG:140 SG:222 R 3 1 1 21 2 2 0 15.0000 0.3387 CA:139 CA:250 R 3 1 1 22 2 2 0 17.0000 0.3387 CA:139 CA:250 R 3 1 1 21 2 2 0 15.3000 0.3387 CB:139 CB:250 R 3 1 1 22 2 2 0 17.3000 0.3387 CB:139 CB:250 R 3 1 1 21 2 2 0 10.0000 0.3387 CA:117 CA:292 R 3 1 1 21 2 2 0 6.00000 0.3387 N:117 N:292 R 3 1 1 27 2 2 0 8.00000 0.3387 CB:117 CG:208 R 3 1 1 27 2 2 0 10.0000 0.3387 CB:117 CG:208 R 3 1 1 27 2 2 0 8.00000 0.3387 CB:117 CG:211 R 3 1 1 27 2 2 0 10.0000 0.3387 CB:117 CG:211

as I mensioed before, the program is not identifying the the SG:140 CG:211, I think it is not identifying gama atoms......I dont know that how i am writing the gamma atom is wrong ???

If i removed these lines from the restrain file, the program is getting core dumped.

can you please help me out this problem.

Thanking you

regards,
Praveen

On Wed, 17 Nov 2004 16:32:54 -0800
  wrote:
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Today's Topics:

1. Re: RE: [modeller_usage] wrong topology for the ligand?
     (Modeller Caretaker)
2. Re: RE: [modeller_usage] wrong topology for the ligand?
     (Cvetan Stojkoski)


----------------------------------------------------------------------

Message: 1
Date: Wed, 17 Nov 2004 16:16:13 -0800
From: Modeller Caretaker <>
Subject: Re: RE: [modeller_usage] wrong topology for the ligand?
To: Youbin Tu <>
Cc: 
Message-ID: <>
Content-Type: text/plain; charset=us-ascii

On Wed, Nov 17, 2004 at 05:25:09AM -0500, Youbin Tu wrote:
Thanks for your reply, which help me a lot. But for my specific situation, the ligand I am trying to use is phenacetin which did not exist in the template pdb file. Or to say, we created it so as to make it docked in the active site by using some NMR restraints. We expected to see some interactions between the ligand and the active site which will make the active site show a differnt look from what it is when no ligand is bound.

Yes - if there is no template, you will have to define parameters for
the ligand.

Now I was really confused, if the ligand can not have correct connectivity, how can we expect to see the interactions between the ligand and the enzyme?

You misunderstand me. Modeller knows the connectivity - it reads it from the topology file - but it doesn't write it to the final model PDB file,
so your PDB viewer cannot read the connectivity.

Again, why the ligand does not show correctly, you know , we build the phenacetin in Builder module in InsightII and output it as a RTF file, then append it to the top_heav.lib file.

The RTF file only defines the topology. It doesn't define the parameters. These need to be put into par.lib. This is the case for any
molecular mechanics package, not just Modeller.

Another question is whether does the RTF file provide enough connectivity information for the ligand?

Certainly. All connectivity for the ligand is included in the RTF (residue topology file) but you need the parameters as well. If InsightII has parameters defined for your ligand, you will need to save
them as well, and put them into Modeller's par.lib file.

Note that the topology only defines bonding interactions, i.e. covalent bonds within the ligand or protein. Interactions between the ligand and the protein are non-bonding, and are not described here - you'd use VDW
or electrostatic interactions for that.

Or is it because of the special restraints we applied in MODELLER which
make the connectivity changed?

They won't change your topology, but of course, if you have a bond interaction which clashes with a user restraint, Modeller will try to
compromise.

	Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage


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Message: 2
Date: Thu, 18 Nov 2004 11:01:34 +1030
From: Cvetan Stojkoski <>
Subject: Re: RE: [modeller_usage] wrong topology for the ligand?
To: 
Message-ID:
	<>
Content-Type: text/plain; charset=ISO-8859-1

Quoting Youbin Tu <>:

Hi Alicia, Ben:
   Thanks for your reply, which help me a lot.
But for my specific situation, the ligand I am trying to use is phenacetin which did not exist in the template pdb file. Or to say, we created it so as to make it docked in the active site by using some NMR restraints. We expected to see some interactions between the ligand and the active site which will make the active site show a differnt look
from what it is when no ligand is bound.

You have used NMR perturbation data to dock a ligand into the active site? You could simulate a ligand-induced conformational change in the receptor just by doing some MD on your complex. I recommend NAMD. However, AMBER will probably work better for you since your compound has an aromatic ring.

Now I was really confused, if the ligand can not have correct connectivity, how can we expect to see the interactions between the ligand and the enzyme? I mean how the follwong refinement steps which is involved with minimization and molecular dynamics correctly dealt with the ligand and the interaction between the ligand and the enzyme?

MD packages rely on complete topology/parameter sets. You can use XPLO2D to predict a lot of this information. However, be aware that the values are completely derived from the pdb file and will need to be edited. Charges will
also need to be added.

Again, why the ligand does not show correctly, you know , we build the phenacetin in Builder module in InsightII and output it as a RTF file, then append it to the top_heav.lib file. The molecule looks very reasonable in InsightII, but after calculation by MODELLER , the ligand looked weird. So, any other program can view RTF file so as to have a check the connectivity of the ligand is reasonably good or not? Or if
the parameters are incomplete, how to make it complete?

Although we have InsightII, I have never built an RTF file with it. I'm guessing it works similar to XPLO2D. Therefore you will most certainly have to edit angle and charge terms. However, you'd think that bonding would be correct.

Another question is whether does the RTF file provide enough connectivity information for the ligand? Or is it because of the special restraints we applied in MODELLER which make the connectivity changed? You know,we even tried to use the ligand without any
restraints, the result still looked weird?

To check if your RTF file provides correct connectivity, pass it through X-PLOR along with your pdb file to produce a psf. You can then view your psf file in VMD to make sure your connectivities are correct. Otherwise just go through the
topology manualy.

Basically, we just want to build a new ligand with some experimental restraints in the active site of a enzyme. If the ligand looked werid, we have to doubt whether the interaction between the ligand and the enzyme is reliable or not? So, we have to know which step create this
problem?

If you already have the structure of the protein you are docking to then I wouldn't recommend using MODELLER to dock your ligand and observe ligand-induced
confomrational changes. Do MD.

1. building the ligand (RFT file)? We did not give enough connectivity
information?
2. running MODELLER? Since there is no restraints to confine the bond or angles for the ligand or the restraints are conflicting with each
other which make the ligand broken?
3. outputting file from MODELLER? Assumed that all the above is good, the only problem is that MODDLER only give the cooridinates of the atoms instead of the relationship ( connectivity) between atoms? Hope I have well explained my problems? And I also attached my RTF
file for phenacetin.
Finally, thanks for your guys' kind help. Anyone's reply in this
topic will be highly appreciated.
  Hope for the best.

youbin


Sorry I didn't go through your RTF file but its laborious work even with the smallest of compounds. Best create the psf file and then visualize it in VMD.


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