On Tue, Apr 7, 2015 at 8:54 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear Prof. Case and Amber users,
> Thanks for the suggestions. How can I use the ff14SB without access to
> Amber14?
>
> Based on these suggestions I have tried to use a short fix as follows:
>
> I have deleted these atoms with error message from the pdb (new pdb
> attached) and removed the atom connection information with the hope that
> leap will fix them automatically.
> Then reran the same set of commands from the leap.in file and it has saved
> the param and inpcrd files (attached), but the partial charge is still
> there.
> Is it likely due to cause problems while running the MD simulation?
>
It won't cause problems that will be easy for you to see (i.e., it won't
cause the system to 'blow up'. However, it is an unphysical model (how can
you have only part of an electron?).
All of the standard amino acid and nucleic acid residues have integer
charges, with the exception of 3'-terminal and 5'-terminal nucleic acid
residues (and the sum of the 3' and 5' charges is -1). So unless you
somehow only have 1 terminal nucleotide, the non-integer charge is caused
by a poor charge definition on whatever residue or residues you
parametrized.
You should revisit the Fe complex in your system to determine why your
charges are non-integral.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 07 2015 - 06:30:07 PDT
