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From: Kenley Barrett <kenley.barrett.gmail.com>

Date: Thu, 30 Mar 2006 13:46:49 -0600

Dear Ilyas,

Thank you very much for your reply. I've attached the pdb file of my

structure. It's a methylated histidine with blocking groups added in order

to simulate the environment of a protein.

I agree that restraining atoms 1-20 to charge 0 when everything but the

hydrogens is frozen seems nonsensical. I made this choice because I've been

trying to duplicate the charge fitting procedure of Duan et al. 2003 (so

that my library file will be compatible with the 2003 force field). In their

article they state that in the second fitting "the charges of the terminal

blocking groups and those of heavy atoms were fixed". Assuming that "heavy

atoms" meant everything but hydrogen, I ran a fitting according to this

description. But my initial attempt resulted in a charge of about .12 on the

non-blocking-group atoms, which is problematic because these atoms need to

have a charge of 0 in order to make a usable library file. So a colleague

advised me to do the same procedure, except adding a constraint that the

non-blocking-group atoms had to add up to 0.

I am very confused at this point about how to accurately duplicate the Duan

et al. method while obtaining a 0 charge on non-blocking-group atoms. I'm

not sure I understand your advice that I should add the constraint in the

first fit and not the second one--wouldn't that allow the charges to move

away from a state in which they add up to 0? And regarding your advice that

I should not freeze the carbon atoms, I am just concerned that that would

not agree with the resp fitting used for the 2003 force field. Does anyone

have any experience doing resp fitting when trying to create library files

using the 2003 methods? Would it be okay to just use the resp fitting

procedure automatically created by respgen (which differs from what is

described in the Duan et al. article)?

Please let me know any suggestions that you have. I'm very grateful for your

thoughts.

Kenley

On 3/30/06, Ilyas Yildirim <yildirim.pas.rochester.edu> wrote:

*>
*

*> Hi Kenley,
*

*>
*

*> I think u should use the restraints on the first fit; not on the second
*

*> one. Most of the atom charges on the second fit are frozen; only the
*

*> H-atoms are recalculated. So, having constrainst on the first 20 atoms
*

*> to have a total zero charge does not have any meaning.
*

*>
*

*> But still, I am not sure if it is correct what u have for the second fit.
*

*> What is the structure? U equivalence the H-atoms which are bound to the
*

*> same carbon, but u froze the charge of the C-atom in the second fit. U
*

*> should recalculate the whole group in the second fit; both the C-atoms
*

*> and H-atoms that are needed to be equilivalenced. Can u send a .pdb
*

*> file of the structure u are dealing?
*

*>
*

*> Best,
*

*>
*

*> On Thu, 30 Mar 2006, Kenley Barrett wrote:
*

*>
*

*> > Dear AMBER community,
*

*> >
*

*> > I am having some difficulties with resp. I want to do a second-stage
*

*> resp
*

*> > fitting in which atoms 1-20 are restrained to have a net charge of 0.
*

*> > However, once I've put the resp charges in a prep file and loaded it
*

*> into
*

*> > xleap, the charge of these atoms comes out to be 0.1230, not 0.
*

*> >
*

*> > I created the constraints in my resp2 input file based on the peptoid
*

*> > example in /opt/local/amber8/examples/resp_charge_fit/. The &cntrl
*

*> namelist
*

*> > is the same as what is automatically created by respgen (I've discovered
*

*> > that ioutopt needs to equal 1 in order for AMBER to go through all the
*

*> steps
*

*> > to make a working prep file).
*

*> >
*

*> > Here are the first and second stage resp input files:
*

*> >
*

*> > First stage input file:
*

*> > First resp fitting for methylated histidine, following Duan et al.
*

*> > procedure.
*

*> >
*

*> > &cntrl
*

*> >
*

*> > nmol = 1,
*

*> > ihfree = 1,
*

*> > ioutopt = 1,
*

*> >
*

*> > &end
*

*> > 1.0
*

*> > Resp charges
*

*> > 0 26
*

*> > 7 0
*

*> > 1 0
*

*> > 6 0
*

*> > 6 0
*

*> > 8 0
*

*> > 1 0
*

*> > 6 0
*

*> > 1 0
*

*> > 1 0
*

*> > 6 0
*

*> > 7 0
*

*> > 6 0
*

*> > 1 0
*

*> > 7 0
*

*> > 6 0
*

*> > 1 0
*

*> > 1 0
*

*> > 1 0
*

*> > 6 0
*

*> > 1 0
*

*> > 6 0
*

*> > 8 0
*

*> > 1 0
*

*> > 7 0
*

*> > 1 0
*

*> > 1 0
*

*> >
*

*> >
*

*> > Second stage input file:
*

*> > Second fitting for methylated histidine, following Duan et al. procedure
*

*> > except
*

*> > restraining the non-blocking atoms to a total zero charge.
*

*> >
*

*> > &cntrl
*

*> >
*

*> > nmol = 1,
*

*> > ihfree = 1,
*

*> > ioutopt = 1,
*

*> > iqopt = 2,
*

*> > qwt = 0.001,
*

*> >
*

*> > &end
*

*> > 1.0
*

*> > resp charges
*

*> > 0 26
*

*> > 7 -99
*

*> > 1 0
*

*> > 6 -99
*

*> > 6 -99
*

*> > 8 -99
*

*> > 1 0
*

*> > 6 -99
*

*> > 1 0
*

*> > 1 8
*

*> > 6 -99
*

*> > 7 -99
*

*> > 6 -99
*

*> > 1 0
*

*> > 7 -99
*

*> > 6 -99
*

*> > 1 0
*

*> > 1 16
*

*> > 1 16
*

*> > 6 -99
*

*> > 1 0
*

*> > 6 -99
*

*> > 8 -99
*

*> > 1 -99
*

*> > 7 -99
*

*> > 1 -99
*

*> > 1 -99
*

*> > 20 0.0
*

*> > 1 1 1 2 1 3 1 4 1 5 1 6 1 7
*

*> > 1 8 1 9 1 10 1 11 1 12 1 13 1 14 1
*

*> > 15 1 16 1 17 1 18 1 19 1 20
*

*> >
*

*> >
*

*> > Here is the -t output of the second stage fitting:
*

*> >
*

*> > -0.030630 0.030630 0.002225 0.457386 -0.567234 0.115050 -0.136863
*

*> > 0.094573 0.094573 0.173194 -0.449827 0.022620 0.156302 0.161476 -
*

*> > 0.180110 0.099700 0.099700 0.099700 -0.302310 0.181925 0.335545 -
*

*> > 0.538195 0.053203 -0.593932 0.360673 0.260624
*

*> >
*

*> >
*

*> > Strangely, if you add up the charges of atoms 1-20, the net charge is
*

*> > actually 0.12208 rather than 0.1230--is this kind of difference normal
*

*> after
*

*> > reading information into XLeap? But regardless of whether the charge is
*

*> > 0.12208 or .1230, I can't use this--I need to find a way to make the
*

*> charges
*

*> > of atoms 1-20 equal 0.
*

*> >
*

*> > I would be very grateful for any suggestions. Thank you in advance for
*

*> your
*

*> > help.
*

*> >
*

*> > Sincerely,
*

*> > Kenley
*

*> >
*

*>
*

*> --
*

*> Ilyas Yildirim
*

*> ---------------------------------------------------------------
*

*> - Department of Chemisty - -
*

*> - University of Rochester - -
*

*> - Hutchison Hall, # B10 - -
*

*> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
*

*> - http://www.pas.rochester.edu/~yildirim/ -
*

*> ---------------------------------------------------------------
*

*>
*

*> -----------------------------------------------------------------------
*

*> The AMBER Mail Reflector
*

*> To post, send mail to amber.scripps.edu
*

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*

*>
*

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Received on Sun Apr 02 2006 - 06:10:13 PDT

Date: Thu, 30 Mar 2006 13:46:49 -0600

Dear Ilyas,

Thank you very much for your reply. I've attached the pdb file of my

structure. It's a methylated histidine with blocking groups added in order

to simulate the environment of a protein.

I agree that restraining atoms 1-20 to charge 0 when everything but the

hydrogens is frozen seems nonsensical. I made this choice because I've been

trying to duplicate the charge fitting procedure of Duan et al. 2003 (so

that my library file will be compatible with the 2003 force field). In their

article they state that in the second fitting "the charges of the terminal

blocking groups and those of heavy atoms were fixed". Assuming that "heavy

atoms" meant everything but hydrogen, I ran a fitting according to this

description. But my initial attempt resulted in a charge of about .12 on the

non-blocking-group atoms, which is problematic because these atoms need to

have a charge of 0 in order to make a usable library file. So a colleague

advised me to do the same procedure, except adding a constraint that the

non-blocking-group atoms had to add up to 0.

I am very confused at this point about how to accurately duplicate the Duan

et al. method while obtaining a 0 charge on non-blocking-group atoms. I'm

not sure I understand your advice that I should add the constraint in the

first fit and not the second one--wouldn't that allow the charges to move

away from a state in which they add up to 0? And regarding your advice that

I should not freeze the carbon atoms, I am just concerned that that would

not agree with the resp fitting used for the 2003 force field. Does anyone

have any experience doing resp fitting when trying to create library files

using the 2003 methods? Would it be okay to just use the resp fitting

procedure automatically created by respgen (which differs from what is

described in the Duan et al. article)?

Please let me know any suggestions that you have. I'm very grateful for your

thoughts.

Kenley

On 3/30/06, Ilyas Yildirim <yildirim.pas.rochester.edu> wrote:

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