Dear Users,
Problem has been resolved by adding the radius of Fe in the mdread.F90 file
as :
else if (atomicnumber .eq. 26) then
! Fe radius
x(L165-1+i) = 1.30d0 + 1.4d0
else
..and recompiling amber serial.
Regards
Kshatresh
On Sun, Mar 23, 2014 at 7:57 PM, Kshatresh Dutta Dubey
<kshatresh.gmail.com>wrote:
> Dear Users,
>
> I am using MMPBSA.py of amber 12. I am calculating the residue wise
> decomposition for a Fe containing protein which failed due to *bad atom
> type: fe.* I am following the previous suggestion by Jason and Bill
> Miller as http://archive.ambermd.org/201101/0220.html and modified that
> patch file according to the fe radius, but unfortunately there is no
> mdread.f file in my $AMBERHOME/src/sander therefore patching gives error:
>
> can't find file to patch at input line 3
> Perhaps you used the wrong -p or --strip option?
> The text leading up to this was:
> --------------------------
> |--- src/sander/mdread.f 2010-04-26 08:21:23.000000000 -0400
> |+++ src/sander/mdread.f 2011-01-12 16:22:07.801623229 -0500
> --------------------------
> File to patch: sodium_gb.patch
> patching file sodium_gb.patch
> Hunk #1 FAILED at 1841.
>
> In my ..src/sander there are mdread.F90, mdread.LES.o and mdread.o files.
> Please suggest me to apply a successful patch for this.
> Thanks in advance
> Kshatresh
> --
>
>
>
--
With best regards
************************************************************************************************
Dr. Kshatresh Dutta Dubey
Post Doctoral Researcher,
c/o Prof Sason Shaik,
Hebrew University of Jerusalem, Israel
Jerusalem, Israel
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Received on Sun Mar 23 2014 - 14:00:02 PDT
