Re: [AMBER] problem

From: Billy Miller III <>
Date: Sun, 14 Mar 2010 09:18:20 -0500

The error suggests that you are having prmtop inconsistency problems. Check
that your prmtops are consistent with one another. The solvated prmtop
should have all the water molecules in it (when you set initial_traj=0).
Make sure that the receptor and ligand prmtop residues are the same as the
script is guessing. If you are including water or ions in any of the prmtops
(excluding the solvated complex prmtop) then the script will probably not
correctly guess the residues masks and you will have to set the mask

I hope that helps.

-Bill Miller III

On Sun, Mar 14, 2010 at 5:56 AM, s. Bill <> wrote:

> Dear AMBERI am trying to use to calculate the binding energy,
> where is not available for my system because of existence of
> zinc ion in my system. (I do know I can implement it in
> file).But, the problem for is that, I have
> submitted my file as following
> Input file:Input file for running PB and GB in parallel&general
> endframe=20, verbose=1, /&gb igb=2, saltcon=0.000/&pb istrng=0.000, /
> It gives me an output without a calculations:|Input file for running PB and
> GB in parallel|&general| endframe=1, verbose=1,|/|&gb| igb=2,
> saltcon=0.000|/|&pb|
> istrng=0.000,|/|--------------------------------------------------------------|Solvated
> complex topology file: SolvatedComplex.prmtop|Complex topology file:
> Complex.prmtop|Receptor topology file: Receptor.prmtop|Ligand
> topology file: Ligand.prmtop|Initial mdcrd(s):
> Data.mdcrd||Best guess for receptor mask: ":1-292"|Best guess for ligand
> mask: ":293"|Ligand residue name is "X1"||Calculations performed using 1
> frames.|Poisson Boltzmann calculations performed using internal PBSA solver
> in sander.||All units are reported in
> kcal/mole.--------------------------------------------------------------------------------------------------------------------------------------------------------------
> I have followed the thread discussing this problem on AMBER list,
> so I tried using initial_traj=1 without specifying -sp prmtop file. But, it
> gives me the following error:Error: Sander output is missing values! BOND
> = ************* ANGLE = 255832.2695 DIHED = 9628.0187
> How can I solve this issue?Also, I was wondering should I include the
> crystallic water molecules and ions in my receptor prmtop file.Thanks in
> advanceS. Bill
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Received on Sun Mar 14 2010 - 07:30:02 PDT
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