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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On May 14, 2012, at 6:01 PM, Xin Geng <xingeng2011.berkeley.edu> wrote: > On Mon, 14 May 2012 17:10:10 -0700, Jason Swails <jason.swails.gmail.com> > wrote: >> On Mon, May 14, 2012 at 3:55 PM, Xin Geng <xingeng2011.berkeley.edu> > wrote: >> >>> >>> >>> Dear all, >>> >>> I want to implement a solvation energy function >>> HPMF(Hydrophobic Potential of Mean Force[1])in Amber in order to use >>> calculate thermodynamics integration of Amber+GB+HPMF. I wrote a > program >>> to >>> implement HPMF. I enclosed my program to this email. >>> >>> However I have >>> trouble in compiling my program with the Amber package. So, I want to > ask >>> what modification I should to do with Amber Package to call the >>> subroutines >>> of my program. >>> >> >>> From what I can tell, you wrote a module. A couple comments. Include > the >> dprec.h header (you seem to have done this already, but look at other >> source files to see how this header is included -- i.e. #include >> "../include/dprec.fh") >> >> This header defines a macro _REAL_ which you should use to define all >> floating point data types (don't use real). This really only works with >> double precision at this point. I think this is safer than using "real" >> and "real*8" like you do... >> >> Afterwards, make sure your source code file is in $AMBERHOME/src/sander, >> then run the command "make depend" in order to update the dependencies. >> >> Other than these comments, I think you would need to provide details > about >> exactly what you did and what error messages you got. >> >> HTH, >> Jason >> >> P.S. -- you should also tell us what version of Amber you are trying to > add >> this to, since the exact instructions depend on that version. > > Hi Jason, > > Thanks for your help! > > I copy my file into $AMBERHOME/src/sander and include some header by > referring icosasurf.f, such as assert.h, dprec.h and memory.h. > I try to add this file to Amber10. > I'll show you what I've done as follows: > (1) Add "use genhpmf, only : init_hpmf" into subroutine force (Line 22 of > force.f) and "call init_hpmf(x,ix,ih,natom,nbona)" into subroutine > force(Line 921 of force.f) > (2) Add " use genhpmf !for HPMF calculation" into subroutine egb(Line 172 > of egb.f) and "if" from line 1614 of egb.f > > if (gbsa == 3) then > > !-----calculate hpmf instead of sasa > !return value is esurf, teh file is ehpmf.f > > totsasa = 0 > esurf = ehpmf() > end if !(gbsa == 3) > > When I use "make serial", the following errors show up: > > gfortran -c -O3 -fno-range-check -fno-second-underscore -ffree-form -o > egb.o _egb.f > In file _egb.f:243 > > use genhpmf !for HPMF calculation > 1 > Fatal Error: Can't open module file 'genhpmf.mod' for reading at (1): No > such file or directory > make[1]: *** [egb.o] Error 1 > make[1]: Leaving directory `/home1/xingeng/HPMF/Amber10/src/sander' > make: *** [serial] Error 2 > > Thanks, > > Xin > > > > _______________________________________________ > 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/amberReceived on Mon May 14 2012 - 19:30:02 PDT