Re: [AMBER] which part of source code implementing GB/SA simulations?

From: Xin Geng <>
Date: Tue, 14 Aug 2012 20:48:24 -0700

Dear dac,

Sorry , I just find some content missing in my last email.

I look at Amber10.


On Tue, 14 Aug 2012 22:30:49 -0400, case <> wrote:
> On Tue, Aug 14, 2012, Xin Geng wrote:
>> I want to read the source code for GB/SA simulations and
>> find file egb.f. In the subroutine egb(x,f,...,...), I find the
>> ==
>> 2) then " and "if (gbsa ==1) then" . I think they are use to control
>> different models. Now what I want to do is to add another "if" sentence
>> to
>> use another model, e.g. "if (gbsa == 3) then call XXX"(XXX is the
>> subroutine for my model). But when I change the code it seems nothing
>> happens. For example, I add "esurf = 1.0d0" after "# include
>> 'gbsa.h'",but
>> when I run "minimization", the result shown in "mdinfo" is the same as
>> before.(Actually, no matter what I add to change the value of esurf and
>> totsasa after "# include 'gbsa.h'" , the value of "esurf" shown in
>> "mdinfo"
>> is the same.)
> We need more details, starting with which version of Amber you are
> at. When you say you added "esurf=1.0" after "#include gbsa.h", do you
> mean
> immediately after? Whatever value you assign to esurf immediately after
> the include line will be overwritten by the "esurf = surften*totsasa"
> shortly
> after that.
> Of course, for debugging purposes, you should print out esurf
> right at that point in the code, to check that it is not being changed
> somewhere else before being printed in the mdinfo file. Unless you are
> willing and able to do such basic programming tasks, I doubt that people
> the list will be able to help much. See if you can get one of the many
> experienced people in your group to look at your code and provide some
> immediate feedback.
> ...good luck...dac
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Received on Tue Aug 14 2012 - 21:00:03 PDT
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