Re: [AMBER] problem

From: s. Bill <>
Date: Mon, 15 Mar 2010 09:00:23 +0000 (GMT)

Dear AMBERThanks so much for your help.In fact, I found I made a mistake in my prmtop files.I was wondering,  the following masks in the output dat file of calculation have been taken based on which prmtop file (Complex,Solvated Complex, or simulation.mdcrd file) in case, these files are not have the same residues in the same order.
|Best guess for receptor mask:   ":1-176"|Best guess for  ligand  mask:   ":177"|Ligand residue name is "X1"
In other words, is it a problem if my solvated_complex.prmtop doesn't have the same sequential residues as in complex.prmtop, where there are some water molecules between the end of the receptor and the ligand, but I removed these water molecules and rebuilt my complex.prmtop but all my mdcrd data has been generated based on solvate_complex.prmtop with water between receptor and ligand.I think uses ptraj to extract snapshots from mdcrd and then strip out the water molecules, so in this case there will no be a difference between my prmtop files, am I right?Thanks again for your help.Sincerely;S. Bill
--- On Sun, 14/3/10, Jason Swails <> wrote:

From: Jason Swails <>
Subject: Re: [AMBER] problem
To: "AMBER Mailing List" <>
Date: Sunday, 14 March, 2010, 16:47

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

Try visualizing your system.  Look at the mdcrd files created by in some type of visualization program with the corresponding
prmtop files (VMD works well).  This result is probably due to the
fact that the prmtop files and coordinate files are not matching up
(so if you try to visualize them, you will get a mess).

Good luck!

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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Mon Mar 15 2010 - 02:30:07 PDT
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