[gmx-users] regarding ligands in proteins

[Daan van Aalten]

Hi Luke

It's not clear from your message if you are starting from a
crystallographically defined complex of glucose with the glucose binding
protein. If so, use the file you got from the PRODRG server, and specify
that together with your ffgmx.* when you run pdb2gmx.

If you do not have a complex, you need to use a program like DOCK/AUTODOCK
first to "generate" the complex, then run as above.

If you have generated the glucose topology from scratch with PRODRG (i.e.
using the ASCII drawing, which is preferred) you can use the attached
FORTRAN jiffy to "swap" atomnames after you have approximaetly positioned
the PRODRG glucose over the PDB glucose.

hope this helps

Daan


On Sun, 7 Oct 2001, Luke Czapla wrote:

> 
> Greetings GROMACS user list:
> 
>   I am a graduate student working on setting up a simulation of a
> glucose-binding protein.  The glucose is not covalently linked.  I have a
> topology file for the glucose using the PRODRG server and a modified PDB
> file for the protein without the glucose residue as well as the original
> one with the glucose labeled GLC.
>   Has anyone had experience with a system similar to this?  I'd like to
> place the glucose inside the protein before energy minimization and I have
> looked all through the documentation for genbox and pdb2gmx and found
> nothing to do this.  Any help would be greatly appreciated!
> 
> cheers,
> Luke Czapla
> 
> 
> 
> 
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

        O     C           O     C         Visit the PRODRG server to take 
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O   
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "         
       O         
-------------- next part --------------
      PROGRAM DELWAT

      IMPLICIT NONE

      CHARACTER*80 SDUM, NAM1,NAM2
      CHARACTER*30 HACK1(10000),HACK2(10000)
      CHARACTER*20 LAST1(10000),LAST2(10000)
      REAL X1(10000),Y1(10000),Z1(10000),
     +     X2(10000),Y2(10000),Z2(10000),XI,YI,ZI,D,ML
      INTEGER I,J,K,NAT1,NAT2

      CALL GETARG (1,NAM1)
      CALL GETARG (2,NAM2)

      OPEN (1,FILE=NAM1,STATUS='OLD')
      OPEN (2,FILE=NAM2,STATUS='OLD')

      NAT1=0
   10 READ (1,1000,END=20) SDUM
      IF (SDUM(1:4).EQ.'ATOM') THEN
        NAT1=NAT1+1
        READ (SDUM,1011) HACK1(NAT1),
     +  X1(NAT1),Y1(NAT1),Z1(NAT1),LAST1(NAT1)
      END IF
      GOTO 10
   20 CONTINUE
      WRITE (0,*) NAT1,' ATOMS in file 1'

      NAT2=0
   30 READ (2,1000,END=40) SDUM
      IF (SDUM(1:4).EQ.'ATOM') THEN
        NAT2=NAT2+1
        READ (SDUM,1011) HACK2(NAT2),
     + X2(NAT2),Y2(NAT2),Z2(NAT2),LAST2(NAT2)
      END IF
      GOTO 30
   40 CONTINUE
      WRITE (0,*) NAT2,' ATOMS in file 2'


    
      DO I=1,NAT1
         ML=999999.0
         DO J=1,NAT2
            D=SQRT((X1(I)-X2(J))**2 + 
     +             (Y1(I)-Y2(J))**2 + 
     +             (Z1(I)-Z2(J))**2)
             
            IF (D.LT.ML) THEN
C               WRITE (6,*) D
               ML=D
               HACK1(I)=HACK2(J)
            END IF
         END DO
         WRITE (6,1011) HACK1(I),X1(I),Y1(I),Z1(I),LAST1(I)
      END DO
      WRITE (6,1020)

 1000 FORMAT(A80)
 1011 FORMAT(A30,3F8.3,A20)
 1012 FORMAT('HBOND ',A30,'  ',A30)
 1020 FORMAT ('END')
      END