Re: [AMBER] Thermodynamic Integration with pmemd, for explicit solvent models

From: Roma Mukhopadhyay <>
Date: Sun, 1 Oct 2017 23:54:40 +0000

Hi David,

Thanks for previous reply.

Below is the size for the solvent box:

 Solute vdw bounding box: 8.113 11.623 5.818
  Total bounding box for atom centers: 36.716 36.716 36.716
      (box expansion for 'iso' is 31.3%)
  Solvent unit box: 18.774 18.774 18.774
  Volume: 26825.938 A^3 (oct)
  Total mass 13249.786 amu, Density 0.820 g/cc

Is the size of box too big to get the error? How can I change the number of water molecules being added?

I have an initial molecule that I am solvating using leap. I use that molecule in another leap to generate the the prmtop and inpcrd files, having the respective parameters of the two molecules by changing the charges, of one molecule. Attached is the zip file containing the tleap files.

Please let me know where I am wrong, and what I should be doing instead.


From: David A Case <>
Sent: Sunday, October 1, 2017 8:08:25 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Thermodynamic Integration with pmemd, for explicit solvent models

On Sun, Oct 01, 2017, Roma Mukhopadhyay wrote:
> ERROR: nfft1 must be in the range of 6 to 512!" and "ERROR:
> fft_blk_y_divisor must be in the range of 2 to 1!
> Is this issue related to the presence of multiple TER cards in the pdb
> file containing the initial molecules?


How big is your periodic box? This error likely comes from having a very
large (or possibly, very small) box.


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Received on Sun Oct 01 2017 - 17:00:02 PDT
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