[gmx-users] pdb2gmx - .top missing values

Dallas Warren dallas.warren at vcp.monash.edu.au
Tue Oct 8 06:36:04 CEST 2002


 >Did you add the bonds for the new rtp entry? And did you get any error 
messages when running pdb2gmx?

No error messages.  It generates a .gro, .top and posre.itp file.

Here is a section from what I have added to the .rtp file:

[ CHD ]
  [ atoms ]
; name  type  charge chargegroup
    C18   CH3   0.000     0
    C13    CB   0.000     1
    C12   CH1   0.150     2
    O12    OA  -0.548     2
    H12    HO   0.398     2

  [ bonds 
; atom1 atom2
    C18   C13 

    C13   C12
    C13   C14
    C13   C17
    C12   O12
    O12   H12

So I have put in formation on the atom name, type of atom it is, charge on 
that atom, group of atoms for charge, and then which atoms are linked to 
which.  Is the numbering system on the atoms OK? e.g. C1, C2, O2, H2, C3 
.... etc?

>By the way - there's a program called x2top that can create rtp entries 
>from coordinates...

Thank you for point that one out, should make the process a little less 
painful ;-)

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy
Monash University
dallas.warren at vcp.monash.edu.au
+61 3 9903 9076
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