VMD-L Mailing List

From: Chari, Ravi (ravi.chari_at_uconn.edu)
Date: Thu Oct 18 2007 - 14:52:48 CDT

Hi,

I have two questions.

First, here's the setup. I am using VMD 1.8.5 and APBS 0.5.1 on a two dual core chip AMD Opteron system running WIndows XP 64. My graphics card is NVIDIA 6800 GeForce GT. I have 3.16 GB of RAM.

I started with a protein in PDB format and added partial charges to it. I then saved it in SYBYL MOL2 format and also as a CHARMM COR and PSF file with Accelrys Discovery Studio 1.7.

Now here is where it gets weird and confusing:

1) I used APBS/VMD to obtain a DX file with the SYBL MOL2 format.
2) I used APBS/VMD to obtain a DX file by loading the CHARMM PSF first and then overlaying the COR file.
3) I used APBS/VMD to obtain a DX file by loading the CHARMM COR first and then overlaying the PSF file.

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?

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

1) I opened the SYBL MOL2 file, added the DX to it, and created a SURF/VOL display. I'll call it SURF/VOL A.
2) I opened the same DX file and added the SYBL MOL2 file and created SURF/VOL B.
3) I opened the CHARMM PSF and added the COR and then the same DX and created SURF/VOL C.
4) I opened the same DX and added the CHARMM PSF and then the COR and created SURF/VOL D.
5) I opened the CHARMM COR and added the PSF and then the DX and created SURF/VOL E.
6) I opened the DX and added the CHARMM COR and added the PSF and created SURF/VOL F.

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?

Any help is appreciated.

Thank you.