Dan, hello!
Thank you for link to the bugfix- this fixed my problem.
Could you provide me with the small tutorial on amber tools
In particular I'm intresting in LEAP program for the preparation of my
initial pdb structure for further simulation.
E.g I want to CAP N and C-termii with some groups like ACE or NH2 and build
missing Hydrogens
Also It's not quite understand for me how properly run different amber
tools programs.
E..g from subdirectory /own/Documents/amber11/AmberTools/bin
I can run all programs but from another directory that programs are not
aviable ( I've add the Bin to the path but it didnt work )
Finally as I understood LEAP have GUI. How I can run this one ?
Thanks again,
James
2011/10/30 Daniel Roe <daniel.r.roe.gmail.com>
> Hi,
>
> What version of the gnu compilers are you using? Have you applied all
> of the bugfixes? http://ambermd.org/bugfixesat.html
>
> I think this issue was corrected with bugfix 8.
>
> -Dan
>
> On Sat, Oct 29, 2011 at 1:42 PM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> > Dear Amber, users!
> >
> > I have problems with compilation of the latest version of the Amber tools
> > under Debuan Linux
> >
> > I've used ./configure gnu
> >
> > and after make install I've obtained
> >
> > ake[1]: Entering directory
> `/home/own/Documents/amber11/AmberTools/src/pbsa'
> > cpp -traditional -P -DBINTRAJ amg1r5.f > _amg1r5.f
> > gfortran -c -O3 -mtune=generic -msse -mfpmath=sse -ffree-form -o
> amg1r5.o
> > _amg1r5.f
> > _amg1r5.f:1204.16:
> >
> > ifg,a(jtrst),time,ndjtr,ium,mdjtr)
> > 1
> > Warning: Type mismatch in argument 'jtr' at (1); passed REAL(8) to
> > INTEGER(4)
> > _amg1r5.f:1217.58:
> >
> > call pcol(k-1,ierr,ia,ja,iw,imin,imax,imaxw,icg,ifg,u(irst), &
> > 1
> > Warning: Type mismatch in argument 'ir' at (1); passed REAL(8) to
> INTEGER(4)
> > _amg1r5.f:1224.26:
> >
> > imaxw,ifg,icg,u(irst),time,ierr,irow0,ncolx, &
> > 1
> > Warning: Type mismatch in argument 'ncolor' at (1); passed REAL(8) to
> > INTEGER(4)
> > _amg1r5.f:1232.16:
> >
> > ifg,u(irst),nstcol,ncolx,time,nda,ndja,ium, &
> > 1
> > Warning: Type mismatch in argument 'ncolor' at (1); passed REAL(8) to
> > INTEGER(4)
> > _amg1r5.f:3461.23:
> >
> > external idec,random
> > 1
> > Error: Return type mismatch of function 'random' at (1) (REAL(8)/REAL(4))
> > _amg1r5.f:3029.45:
> >
> > ja(jlo),a(jlo),f(ilo),u(ilo),nsp,a(jhi+1),a(jhi+1), &
> > 1
> > Warning: Type mismatch in argument 'isp' at (1); passed REAL(8) to
> > INTEGER(4)
> > _amg1r5.f:3095.45:
> >
> > ja(jlo),a(jlo),f(ilo),u(ilo),nsp,a(jhi+1),a(jhi+1), &
> > 1
> > Warning: Type mismatch in argument 'isp' at (1); passed REAL(8) to
> > INTEGER(4)
> > _amg1r5.f:3619.17:
> >
> > external cgalf,cgeps,ctime
> > 1
> > Error: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4))
> > _amg1r5.f:3619.23:
> >
> > external cgalf,cgeps,ctime
> > 1
> > Error: Return type mismatch of function 'cgeps' at (1) (REAL(8)/REAL(4))
> > make[1]: *** [amg1r5.o] Error 1
> > make[1]: Leaving directory
> `/home/own/Documents/amber11/AmberTools/src/pbsa'
> > make: *** [serial] Error 2
> >
> > How I can solve that problem?
> >
> > Thank you
> >
> > James
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Postdoctoral Associate
> BioMaPS Institute, Rutgers University
> 610 Taylor Road
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Oct 30 2011 - 01:00:03 PDT
