Re: [AMBER] How to implement a new energy function in AMBER

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 14 May 2012 19:22:58 -0700

Did you do the "make depend" step I mentioned?

--
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
> 
> 
> 
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Received on Mon May 14 2012 - 19:30:02 PDT
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