AMBER Archive (2009)

Subject: Re: [AMBER] number-of-EPS-exceeds-MAXESP

From: Karol Kaszuba (
Date: Sat Jan 10 2009 - 09:27:08 CST

Dear Francois,

First - thanks for the help.

1) "I would strongly suggest you comparing charge values using IOp(6/33=2)
and (6/33=2,6/41=10,6/42=17)..."

   I have already done it - but only for one conformation.
   In case of - IOp(6/33=2) = Fe charge = +0.08.

2) "comparing charge values for different molecular orientations.."

   Well I have been thinking about it but based on the literature I found
that at least for one
   "type of heme" (to which HIS and MET are linked) there are "strict"
    dependencies= bond lengths,angles around Fe which denote optimized
    That's way I am not sure if charges (especially for Fe and atoms close
to Fe) should be
    calculated based on many conformations. Besides I think that in case of
heme=IRON the
    "IOp parameter" is a crucial thing - however this is only my opinion
and I could be wrong...

3) Now about this RESP recompilation.
    Well I don't know FORTRAN. I checked in the web how I should define the
integers and so
    on.. so I tried:
   - 2i5 ---> 2i6 - *segmentation fault*
   - 2i5 ---> 2i7 - *segmentation fault*
     so I asked one person who advised:
  - 2i5 ---> i5i6 - finally RESP worked and charges were fine.

    But I would like to be sure: does this change "2i5 ---> i5i6" is in
agreement with whole
    RESP algorithm? I mean: I changed only "ESP points limit", besides RESP
works as
   "default 2i5"?

4) I can also send you the last version of R.E.D.-III.1 if you wish).

    Well - RED was my first option but I had to use cc-pvtz with GEN keyword
and I didn't
    know how to put cc-pvtz function in RED code + I wasn't sure if I can
modify your code.
    But still I would be grateful if you can send me R.E.D.-III.1.

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