Hi Ross:
I mixed up files, using a pdb that I assumed was saved just after
inpcr/prmtop from leap. Actually, what I used was a pdb from previous
runs so that the number of atoms did not match. When the correct pdb
file is used, prmtop/pdb can be loaded to VMD and the cell geometry
and position directly determined, and namd was happy, too.
As to the cell position, I used the center. The minimization reached
gradient 1.7 very soon and the protein is at the center of the
rectangular box. However, I'll pay quantitative attention to that,
continuing with the A1 tutorial before getting into troubles with the
new system.
Thanks indeed
francesco
On Thu, Oct 20, 2011 at 6:39 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Francesco,
>
>> Just a quick (final) question: do the last line of the .inpcrd file
>> for a rectangular box represent the cellbasisvectors (xyz, first three
>> values) and the center of the box (xyz, last three values)?
>>
>> 64.0352560 68.0597930 61.0211890 90.0000000 90.0000000 90.0000000
>
> It is the box dimensions in X, Y and Z and then the angles alpha, beta, gamma. In this case you have an orthorhombic box so all the angles are 90 degrees.
>
> The origin is normally the corner of the box in AMBER (as opposed to the center of the box in CHARMM). I think I got that the right way around. So the key is what NAMD expects the origin of the box to be. If it expects it to be the corner then probably 0, 0, 0 is the right value. If it expects the center of the box then 32.017628, 34.0298965, 30.5105945.
>
>> I used them in the .conf file:
>> # periodic settings
>> cellBasisVector1 64.0352560 0.0 0.0
>> cellBasisVector2 0.0 68.0597930 0.0
>> cellBasisVector3 0.0 0.0 61.0211890
>> cellOrigin 90.0000000 90.0000000 90.0000000
>>
>> I did that because the .prmtop/.inpcrd of the A1 tutorial saved aafter
>> "solvatebox 1PLC TIP3PBOX 12" let to perform a correct minimization
>> with NAMD-CUDA multiple GTX-580 (juust 1000 steps; I forgot to check
>> the gradient), while they do not open correctly in VMD (just a
>> straigth segment instead of a box, so that I could not measure the
>
> Try using Amber 7 prmtop and Amber Restart as the file format instead of Amber Coordinates. Inpcrd files are considered to be restart files by VMD.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Thu Oct 20 2011 - 13:30:02 PDT
