2010/4/29 Joćo Henriques <joao.henriques.32353.gmail.com>
> I'm 100% sure Resp within AmberTools can handle multi-conformational
> fits. I've done quite a few myself. But I don't know how limited it
> is. I'll run a few tests with less points per each atomic center to
> see if it is due to the cheer size and complexity of my models. I
> provide over 150.000 points for each model (they are 4). So it might
> be too much to handle.
> As a final measure I'll have a serious look at RED. In good truth I
> haven't looked at it more seriously because from what I've read it
> uses AmberTools Resp code. If I can use the code directly why use it
>
It does use the amber resp, which makes it compatible with current amber
charge models. However, recalling the brief glance I gave R.E.D., I believe
it has a series of python (maybe perl?) scripts wrapped around it, and it's
a program devoted to RESP fitting. I do not think it suffers from the
size-limitation you're encountering here, but having never used it I'm not
an authoritative source.
The R.E.D. people are quite responsive on this list regarding applicable
problems, so they're probably very responsive on their own mailing list, and
they have a plethora of tutorials/documentation to help get started.
A quick look at resp.f in $AMBERHOME/AmberTools/src/etc/ (in AmberTools 1.4)
suggests that limits.h in the same directory would be a logical place to
start looking. I don't know if changing those parameters will mess anything
else up (or even fix your problem), but it seems like a reasonable place to
start. Other more knowledgeable people will have to comment further on
this, as my experience with both of these programs is only skin-deep.
Good luck!
Jason
through an intermediate program. (This consideration might be wrong,
> as I said I haven't done any significant research on RED).
>
> If the limitation in Amber's Resp program is proven this becomes
> serious, since it might occur to other users. Some kind of measure
> should be taken. At least inform users about this limitation.
>
> Thanks for all the feedback, I'm always looking forward to receiving
> more input from experienced users.
>
> On Thu, Apr 29, 2010 at 1:10 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > Hello,
> >
> > I'm not sure if RESP included with amber can handle multi-conformational
> > resp fits. I remember reading somewhere that it doesn't, but you said
> that
> > it did for small molecules, so I'm not quite sure.
> >
> > If you're looking to do some heavy-duty multi-conformational RESP
> fitting, I
> > would suggest looking at R.E.D., which is linked to from
> > http://ambermd.org. There has been plenty of discussion about it on
> > the Amber list, and it
> > has more capabilities built in than the resp.f included with amber.
> >
> > Good luck!
> > Jason
> >
> > 2010/4/29 Joćo Henriques <joao.henriques.32353.gmail.com>
> >
> >> They were all GNU. GCC and GFORTRAN. A friend researcher of mine used
> >> PGI with 1.4 version of AmberTools and obtained the same error.
> >>
> >> On Thu, Apr 29, 2010 at 2:33 AM, Mengjuei Hsieh <mjhsieh.gmail.com>
> wrote:
> >> > 2010/4/28 Joćo Henriques <joao.henriques.32353.gmail.com>:
> >> >> It's really confusing. This leads me to suspect that
> >> >> the file size is prohibitive, but if that's the case why isn't there
> >> >> anything written about this on the manual or something. Since I have
> >> >> 99 atoms and I'm calculating the esp with B3LYP/Gen (6-31G(d) and
> >> >> LANL2TZ(f)) with SCF=Tight, Pop(MK,ReadRadii,Full) and
> >> >> IOp(6/33=2,6/41=10,6/42=17) I might have too much points too compute
> >> >> with resp... But again I'm just guessing!
> >> >
> >> > Hi, it is indeed intriguing, what compilers are you using for
> >> > AmberTools? Knowing the kind of compilers might help developers
> >> > tracking down the issues.
> >> >
> >> > Best,
> >> > --
> >> > Mengjuei
> >> >
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> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Apr 29 2010 - 07:00:03 PDT
