> I confirmed that I also found this problem.
>
> I think the biggest problem is not the format of the PDB but how did
> Amber treat those residues during the simulations. If it treat the
> split three moeity of a lipids as a whole , it should be OK. Otherwise,
> it would be a big problem for the simulation results.....
If you could check this I would very much appreciate it. However, it SHOULD
be fine. Those lipids should be bound together and the bonds defined in the
prmtop. Open it in VMD and take a look and see if the bonds are there in the
prmtop.
I believe it is just a bug in leap when writing a pdb file from leap.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri May 11 2012 - 10:30:05 PDT
