[gmx-users] more questions

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 9 09:17:29 CEST 2001

On Tue, 9 Oct 2001, Daan van Aalten wrote:

>Hi Luke
>This is going to be quite difficult. Usually the way these topology
>builders (like pdb2gmx) work is that they need to be able to identify
>certain atoms by their name. For instance, to add the psi torsion
>angle between residues X and Y, one needs X_CA,X_C,Y_N,Y_CA for the next
>psi angle, between Y and Z, one needs Y_CA,Y_C,Z_N,Z_CA
>The problem now is that if you think of your entire complicated 3-amino
>acid thingy as "residue" Y, the atoms Y_CA in the first and second psi
>angle are *not* the same, and as such you cannot build a .rtp entry for
Not so pessimistic. There is another method using the special bonds file
that is also used for Cys-Cys bridges and e.g. Heme-Protein interconnects.
This looks for atoms in two residue types (Ser-GLy in this case) within a
certain distance, and if found makes a bond.

>Once the size limit on PRODRG is gone, one should be able to build entire
>topologies for protein which contain as much of these modifications as you
>want. Perhaps you can test a small section of your protein (< 100 atoms)
>with this chromophore in the middle? If it works I'll try to free some
>time to up the size limit to 10000 or so.
Obviously most users would really welcome this. Hope your algorithm scales

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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