AMBER Archive (2008)

Subject: Re: AMBER: molsurf fails

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Nov 25 2008 - 13:26:14 CST

On Tue, Nov 25, 2008, Arturas Ziemys wrote:
>
> For some frames I get errors like that:
> molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.

Try the following patch to $AMBERHOME/src/mm_pbsa/molsurf.c, the recompile:

diff -u -r10.1 -r10.2
--- molsurf.c 2 Jun 2008 22:15:47 -0000 10.1
+++ molsurf.c 17 Sep 2008 10:47:50 -0000 10.2
@@ -1030,7 +1030,7 @@
   POINT t_ij, t_ik, t_diff;
   REAL_T b_factor, h_ijk, xtest;
   REAL_T w_ijk, w_sin, r_pk2;
- REAL_T sarg1, sarg2;
+ REAL_T sarg1, sarg2, check1, check2, check3, check4;
   POINT b_ijk, r_ib;
   void cross ();
   int i;
@@ -1050,7 +1050,16 @@
   }
 
   sarg1 = (ai->rad + aj->rad + probe_diam) * (ai->rad + aj->rad +
- probe_diam) - d_ij * d_ij;
+ probe_diam) - d_ij * d_ij;
+ /* For rounding to 6 decimal points in case sarg1 < 0 */
+ if(sarg1 < 0){
+ check1 = sarg1;
+ check2 = 0;
+ check3 = fabs(modf( check1 * 1000000, &check2));
+ check4 = (floor(check1 * 1000000) + (check3 < 0.5 ? 1 : 0 ))/1000000;
+ sarg1 = check4;
+ }
+
   sarg2 = d_ij * d_ij - (ai->rad - aj->rad) * (ai->rad - aj->rad);
   assert( sarg1 >= 0.0 );
   assert( sarg2 >= 0.0 );

[This probably should get posted as a bugfix....]

...good luck....dac

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