Hi everybody,
I'm repeating the preparation of topology files for a ligand-receptor complex.
The files have been prepared without tleap issuing any untoward warnings.
On solvating the system, I got
> saveamberparm COMPLEX 2erb_indole_solv.prmtop 2erb_indole_solv.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
!FATAL ERROR----------------------------------------
!FATAL: In file [unitio.c], line 1788
!FATAL: Message: 1-4: cannot add bond 386 874
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.
!
!ABORTING.
I'm rather stuck. Your advice how to overcome this problem would be most welcome.
As I mentioned this is a repeat prep. On earlier occasions I didn't get anything like this. The only thing that I did differently this time was to construct 3 disulfice bonds issuing the commands:
COMPLEX=loadpdb 2erb_indole.pdb
> bond COMPLEX.26.SG COMPLEX.57.SG
> bond COMPLEX.53.SG COMPLEX.104.SG
> bond COMPLEX.95.SG COMPLEX.113.SG
saveamberparm COMPLEX 2erb_indole.prmtop 2erb_indole.inpcrd
and the same for the receptor.
Best regards
George
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Received on Sat Nov 26 2011 - 10:30:03 PST
