Dear Wei,
Thanks for the solution. It is working now.:) I compiled AMBER 8 making
the changes u wrote in your email, and everything is working fine. But I
could not compile AMBER9 (not because of these changes, but something
else).I will send this error message to the AMBER-developers mailing list.
Thanks again.
Best,
On Wed, 2 Nov 2005, Wei Zhang wrote:
> Hi Ilyas,
>
> I think I have found the reason, it is because xleap use a "%1.4lf"
> format to display and save charge. To fix it is easy, I think you
> can do it by yourself, it is in file
>
> amber9/src/leap/src/leap/xaAtomTable.c
>
> line 163:
>
> #define DBLFMT "%1.4lf"
>
> replace it with
>
> #define DBLFMT "%10.6lf"
>
> and if you want to show charge in more precision format via "charge"
> command, you can modify file
>
> amber9/src/leap/src/leap/commands.c
>
> line 2892-2894
>
> VP0(( "Total unperturbed charge: %6.4lf\n", dCharge ));
> /*dPertCharge is now the delta of the charge and not the actual
> perturbed charge*/
> VP0(( "Total perturbed charge: %6.4lf\n", (dCharge+dPertCharge) ));
>
> replace %6.4lf with %10.6lf,
>
> recompile and install xleap by
>
> make
> make install
>
> I think it would fix your problem.
>
> Please do tell me whether it works, since we may want to make a bugfix
> for it.
>
> Sincerely
>
> Wei Zhang
>
> On Fri, 2005-10-28 at 21:26 -0400, Ilyas Yildirim wrote:
> > Dear All,
> >
> > I have calculated the RESP charges for some structures by doing
> > multimolecular charge fitting. I followed the RESP protocol. I have
> > created the .prepi files for these structures using the new RESP charges,
> > and everything is fine; namely, the charges of each structure looks ok.
> > (By ok, I mean the following: The RX5' and RX3' parts add to -1 while the
> > intermediate residues (RX) have -1 charge) Then I have loaded these
> > structures into xleap and entered the perturbed charge information (also
> > the other parameters needed to do perturbation) in the "Edit Selected
> > Atoms" window. In that window, I kept the "unused" parts blank. Then I
> > have saved the structures using saveoff command. Here, I am copy/pasting
> > some part of a file created:
> >
> > .
> > .
> > .
> > "C6" "CM" 0 1 131073 29 6 -0.040620
> > "H6" "H4" 0 1 131073 30 1 0.225025
> > "C3'" "CT" 0 1 131073 31 6 0.176434
> > "H3'" "H1" 0 1 131073 32 1 0.069871
> > "O3'" "OH" 0 1 131073 33 8 -0.660896
> > "H3T" "HO" 0 1 131073 34 1 0.442954
> > !entry.RC3.unit.atomspertinfo table str pname str ptype int ptypex int
> > pelmnt dbl pchg
> > "P" "P" 0 -1 0.0
> > "O1P" "O2" 0 -1 0.0
> > "O2P" "O2" 0 -1 0.0
> > "O5'" "OS" 0 -1 0.0
> > "C5'" "CT" 0 -1 -0.001094
> > "H5'1" "H1" 0 -1 0.002027
> > "H5'2" "H1" 0 -1 0.002027
> > "C4'" "CT" 0 -1 -0.028908
> > "H4'" "H1" 0 -1 -0.000479
> > .
> > .
> > .
> >
> > When I use the command "charge <name of the structure>", it is giving me
> > the expected charge informations. As an example;
> >
> > > charge RC3
> > Total unperturbed charge: -0.6805
> > Total perturbed charge: -0.6805
> > >
> >
> > or
> >
> > > charge RC
> > Total unperturbed charge: -1.0000
> > Total perturbed charge: -1.0000
> > >
> >
> > Now, when I put the 'true' variable into the "unused" parts of the
> > perturbed atoms (in the "Edit Selected Atoms" window), and saveoff the
> > structures, the charges I see in the files are rounded off. As I an
> > example, I am getting the following charges compared to the charges I
> > copy/pasted above:
> >
> > .
> > .
> > .
> > "C6" "CM" 0 1 131073 29 6 -0.040600
> > "H6" "H4" 0 1 131073 30 1 0.225000
> > "C3'" "CT" 0 1 131073 31 6 0.176400
> > "H3'" "H1" 0 1 131073 32 1 0.069900
> > "O3'" "OH" 0 1 131073 33 8 -0.660900
> > "H3T" "HO" 0 1 131073 34 1 0.443000
> > !entry.RC3.unit.atomspertinfo table str pname str ptype int ptypex int
> > pelmnt dbl pchg
> > "P" "P" 0 -1 0.0
> > "O1P" "O2" 0 -1 0.0
> > "O2P" "O2" 0 -1 0.0
> > "O5'" "OS" 0 -1 0.0
> > "C5'" "CT" 0 -1 -0.001100
> > "H5'1" "H1" 0 -1 0.002000
> > "H5'2" "H1" 0 -1 0.002000
> > "C4'" "CT" 0 -1 -0.028900
> > "H4'" "H1" 0 -1 -0.000500
> > .
> > .
> > .
> >
> > The problem is when I check out the total charge of the structures. When I
> > use the "charge" command in xleap for these .lib filed structures, I am
> > getting the following results:
> >
> > > charge RC3
> > Total unperturbed charge: -0.6805
> > Total perturbed charge: -0.6806
> > > charge RC
> > Total unperturbed charge: -1.0000
> > Total perturbed charge: -1.0001
> > >
> >
> > In this example, the difference is small, but in some other examples, the
> > difference is 0.0002 or 0.0003. This happens because of the roundoff. I
> > wonder if I HAVE to use 'true' variables in the "Edit Selected Atoms"
> > window (for the perturbed atoms) if I want to do perturbation simulation.
> > If the answer is yes, how can I solve the problem I am having here?
> > Thanks in advance.
> >
> > Best,
> >
>
--
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/ -
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Received on Thu Nov 03 2005 - 01:53:00 PST
