Fixed the "***" issue in PDB output format by shifting the center of each molecule...

diff --git a/bin/xdrfpdb/xdrf2pdb b/bin/xdrfpdb/xdrf2pdb
index 8b2f50a..2d2cb08 100755 (executable)
Binary files a/bin/xdrfpdb/xdrf2pdb and b/bin/xdrfpdb/xdrf2pdb differ

diff --git a/source/xdrfpdb/src/xdrf2pdb.F b/source/xdrfpdb/src/xdrf2pdb.F
index c33490b..592d552 100644 (file)
--- a/source/xdrfpdb/src/xdrf2pdb.F
+++ b/source/xdrfpdb/src/xdrf2pdb.F
@@ -17,6 +17,7 @@
       external rescode
       logical iblnk
       external iblnk
+      double precision cm(3)
       
       ifreq=1
       is=1
@@ -150,6 +151,20 @@ c       write (*,'(8f10.5)') ((coord(k,j),k=1,3),j=1,isize)
              c(j,i+nres)=coord(j,ii+nres)
            enddo
          enddo
+c Calculate the CM
+         do j=1,3
+           cm(j)=0.0d0
+           do i=1,nres
+             cm(j)=cm(j)+c(j,i)
+           enddo
+           cm(j)=cm(j)/nres
+         enddo
+         do i=1,nres
+           do j=1,3
+             c(j,i)=c(j,i)-cm(j)
+             c(j,i+nres)=c(j,i+nres)-cm(j)
+           enddo
+         enddo
          etot=potE
          write (tytul,'(a,i6)') "Structure",kk
          call pdbout(etot,tytul,9)