VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 18 2007 - 15:08:21 CDT

Hi,
  I can answer several of your questions:

On Thu, Oct 18, 2007 at 03:52:48PM -0400, Chari, Ravi wrote:
[...]
> Now here is where it gets weird and confusing:
[...load same molecule in several file format combinations...]

> It turns out that the DX files are not exactly the same, although the potential values are similar if rounded off to two places after the decimal point. So it's not too big a deal.

[....]
> But my FIRST QUESTION is: shouldn't all DX files be the same?

Unless the data in each of the file formats is verbatim identical and
parsed verbatim identically, the data fed into APBS will be different,
and so the results will differ. The question you should be asking yourself
is whether the charges/radii defined in these various file format combinations
have the same number of significant digits, as this directly impacts what
is sent to APBS.

> The next issue is a little more troubling. I then did the following in VMD:

[...loading various file sets in different combinations and orders...]

> In the first 4 cases, SURF/VOL A,B,C,D are the same. E and F are the same as each other BUT are slightly different from A to D. The problem occurs when you have separate CHARMM topology and coordinate files. The order in which you load them is important. Based on these observations, the correct way is to load the PSF first and then the COR file. This sequence will give the same SURF/VOL as loading a file with both coords and charge info (such as SYBYL MOL2 or PQR).
[....]

> So my 2ND QUESTION is: has anyone else encountered this problem and confirmed this to be the case?
>

The order that you load files in VMD matters when you load multiple
files that contain the same type of information. The file loaded last
typically overwrites the information loaded (or guessed) from earlier
files. So, for example, if you read multiple file formats that contain
charge data, the last one loaded will be determine the final charge data
in VMD.

If you have more questions, let me know.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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