AMBER Archive (2009)

Subject: Re: [AMBER] S-S problem-in protein

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Mon Oct 12 2009 - 17:14:02 CDT

Dear Dr. Jason,

Based on your suggestion, last night I went back and read the tutorial on the mm/pbsa. But there was few tips on this topic-"set default Radii_". Maybe I miss it. Can you give me more details about this, or you can just give me the page number. On the other hand, when I read a tutorial from Bethany, I found IGB =2, is the best for mutation-effect calculation. But he just referred to the GB rather than PB. I guess the big diffrence (-300 (PB) VS -50 (GB)) between PB and GB may attribute to non-convergence (the polar desolvation) to my system. I think using apbs can solve this, by seting smaller grid space. But since using MMPBSA can do the job that apbs does, I still want to solve this problem.

Another problem, I ever found one complex has over big VDW evergy, > +6000
! I guess it may radii clash? But I have minimized this complex, and used autodock calculate it, finding it is ok. What is wrong with this? I found to some complex, MM/PBSA can really make a good job, but to others it.... Anyway, I am still confident to solve these problem using MM/PBSA.

Thanks for your help again!

Best wishes,
Rilei Yu

--- 09年10月12日，周一, Jason Swails <jason.swails_at_gmail.com> 写道：

发件人: Jason Swails <jason.swails_at_gmail.com>
主题: Re: [AMBER] S-S problem-in protein
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年10月12日,周一,下午7:23

If you have already performed the PB calculations, I would use that since
it's formally more exact, but it may be concerning if the values are very
very different.  It's important to be sure that you used the correct radii
set when you created your topology file (see the command "set default
pbradii _____") where you can specify mbondi, mbondi2, bondi, or amber6.
 Each value of igb has its recommended value detailed in the amber manual.
 You also have to be careful that you use the same radii set in each
topology file.  This is a small detail easily overlooked that can greatly
impact your results.

On Mon, Oct 12, 2009 at 5:16 AM, Rilei Yu <yulaomao1983_at_yahoo.com.cn> wrote:

> Dear Dr. Jason,
>
> I still have a problem, after calculating the binding energy of my system,
> I found the PB and GB is really very different. Should I make an average
> value or just select one of the method to make a comparison?
>
> Regards,
>
> Rilei Yu
>
> --- 09年10月12日，周一, Rilei Yu <yulaomao1983_at_yahoo.com.cn> 写道：
>
> 发件人: Rilei Yu <yulaomao1983_at_yahoo.com.cn>
> 主题: Re: [AMBER] S-S problem-in protein
> 收件人: "AMBER Mailing List" <amber_at_ambermd.org>
> 日期: 2009年10月12日,周一,下午2:28
>
> Dear Dr. Jason,
>
> Thanks for your very detailed suggestion, and I will have a try!
>
> Regards,
>
> Rilei Yu
>
> --- 09年10月12日，周一, Jason Swails <jason.swails_at_gmail.com> 写道：
>
> 发件人: Jason Swails <jason.swails_at_gmail.com>
> 主题: Re: [AMBER] S-S problem-in protein
> 收件人: "AMBER Mailing List" <amber_at_ambermd.org>
> 日期: 2009年10月12日,周一,下午12:24
>
> After reading a little about leap and sleap commands in the ambertools
> manual, the automation of disulfide bond creation appears to be unique to
> sleap.  You can turn automatic disulfide bond creation to 'off', 'auto', or
> 'manu'.  If you set it to off, it will not create disulfide bonds.  If you
> set it to 'auto', (which I believe is default) it will create disulfide
> bonds between two sulfurs on CYX residues if they fall within 'disulfcut'
> angstroms of one another.  Disulfcut is a variable you can define that has
> a
> default value of 2.2 angstroms.  If set to 'manu', it'll ask you before
> creating the bonds.  There may be some way of automating this in tleap or
> xleap using bondByDistance, but I would suggest trying out sleap.  Look at
> the commands "disulfide" and "disulfcut" in the ambertools manual (which
> can
> be found quite easily by either googling or perusing www.ambermd.org) for
> more information if you need it.
> All the best,
> Jason
>
> 2009/10/11 Jason Swails <jason.swails_at_gmail.com>
>
> > Rilei,
> > Leap adds hydrogens by default according to a template in
> all_amino94.lib,
> > which is designed to make the process of creating topology files from
> PDBs
> > easy.  However, this makes the different protonation states of various
> > residues slightly more complex (i.e. different protonation states of
> > Histidine, Aspartate, Glutamate, etc.). Thus, each protonation state is
> > given its own residue name.  Cysteine, too, can either be a free residue
> > capped by a hydrogen, or it can be involved in a disulfide bond with
> another
> > cysteine (yielding a cystine).  Thus, a free cysteine has the 3-letter
> code
> > CYS, but each cysteine member of a cystine (cysteine dimer) has the
> 3-letter
> > code CYX according to all_amino94.lib.  Therefore, if you wish to change
> > your cysteines into cystines, change each CYS in the pdb into CYX.
> >
> > In this detail, I may be mistaken, so somebody please correct me if I am,
> I
> > am drawing from recollection of my own experiences adding S-S bonds.  If
> you
> > are using tleap or xleap, you will have to manually add the S-S bonds
> > (either through the 'bond' command detailed in the ambertools manual, or
> by
> > hand in xleap if that's possible, I've never tried that approach).
> However,
> > if you use sleap, I believe that it adds the disulfide bonds for you.
> >
> > Hope this helps,
> > Jason
> >
> > 2009/10/11 Rilei Yu <yulaomao1983_at_yahoo.com.cn>
> >
> > Dear amber users,
> >>
> >> When i load my protein that contains 7 S-S,I found the these disufides
> >> bonds were all open, and one hydrogen is linked to the "S"-atom
> terminal, so
> >> I edit them in the xleap one by one, it is really time consuming,
> because I
> >> will edit many such complex! Do anyone know is there any better approach
> to
> >> solve this problem?
> >>
> >> Thanks for your help!
> >>
> >> Rilei Yu
> >>
> >>
> >>      ___________________________________________________________
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> >>
> >
> >
> >
> > --
> > ---------------------------------------
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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>
>
>       ___________________________________________________________
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> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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