In addition today I've examined Amber tools more carefully
I have some problems:
1- firstly none of the programs from AMberTools dont runs from other
places than ambertools/bin
I've added to path by export
PATH=$AMBERHOME:home/own/Documents/Amber11/ambertools/bin
but this works only ones when I reboot terminal I must to add the above
command again.
2- After compilation I could not find xleaf program ( only console version
of leaf program was presented)
In manual I've found that xleaf must be installed to the Amber11/exe/xleaf
but there are no exe subdir in my amber11 dirrectory :(
I've installed ambertools by the default way presented in manual
is there any possible way to add xleaf to already built ambertools ?
Thanks again
James
2011/10/30 James Starlight <jmsstarlight.gmail.com>
> 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
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 30 2011 - 07:00:03 PDT
