[AMBER] mmpbsa number of atoms issues

From: Ayesha Fatima <ayeshafatima.69.gmail.com>
Date: Sat, 14 Sep 2013 18:44:31 +0800

Dear All,
I am trying to calculate the binding energy for my complex. I run into a
familiar issue of incorrect atom numbers between prmtop and crd files. I
have searched the tutorials and also the mailing list but i cannot find a
specific solution. I am sure it is easy but i am unable to put my finger on

The complex i simulated has water molecules in the binding site which i
want to retain. when i want to generate the prmtop files, i am confused.
the order of the atoms in the complex is protein-ligand-water in binding
site. I prepared the prmtop files for the complex for mmpbsa by stripping
the added water besides the water in the binding site. The prmtop file
prepared for the prtotein alone also has the water in the binding site. The
prmtop file of the ligand is of the ligand only, nothing extra.

Q1 Where should i get the value for the RSTART AND RSTOP AND the LSTART and
LSTOP? Which pdb file to consider. is it the one which is used in the
simulation? This is by far the most confusing part since this the file to
generate the snapshots because when i want to write the RSTART and RSTOP, i
am not sure what should be written.

Q2 How do i account for the water molecules in the binding site? Should
they be removed also when preparing the prmtop files for the mmpbsa?

Q3 Could there be an issue with the order of the complex atoms? Should it
be protein-ligand-water in binding site or protein-water in binding site-

Q4 if i change the order of atoms, should i run the md again? by right i
should, but is there a way around the problem?

i hope someone can explain to me
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Received on Sat Sep 14 2013 - 04:00:03 PDT
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