[gmx-users] Fuse Protein and non Protein Part of Ligand

[Archer]

Hi,

I have a small problem, I have a relatively big ligand (ca 1200Da) and I
want to fuse him (the fragments exist as rtp). And I thought that the online
servers to calculate could be not good enough for that ligand.  For that
reason I have chosen the specbond.dat wa.
Now I am able to fuse the part Non-Protein, Non-Protein and I am able to
make a bond Protein-Protein. This gives a correct file and the bond of
spec-bond is included. 

But now I try the same thing with the same ligand (means also the same rtp
entries with Non-Protein and Protein:

Linking LYS-3 N-9 and PLI-0 C7-117...
Linking LYS-8 N-35 and PLI-0 C7-141...
Linking LEU-1 C-44 and LYS-1 NZ-60...
Linking GALB-0 O1-101 and PLI-0 C1-111...
Linking GALB-0 O1-125 and PLI-0 C1-135...
Start terminus LYS-3: NH3+
End terminus ILE-14: COO-

-------------------------------------------------------
Program pdb2gmx_mpi, VERSION 4.6.5
Source code file: /usr/local/gromacs-4.6.5/src/kernel/pdb2top.c, line: 960

Fatal error:
Residues in one molecule have a different 'bonds' type: 2 and 1
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"With a Lead Filled Snowshoe" (F. Zappa)

I searched long and it's still not clear to me, why this bonds type error is
coming... And it's really only if I try to combine non-protein and protein
rtp entries. If I do with the same method any other combination, then is
there no problem...

Someone knows, why bonds type occurs? 
P.S. PLI is myself build with ATB Server and translated to rtp. But the
error also occurs if I only take Galactose and Protein for testing
reasons...

Ok, clear, the code/method on line 960 compares two values and they are
different, but this helps me not if I don't know which value is not
fitting...

Thank you for your answers. Or suggestions to solve the problem... 


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