Hello All,

I hope this is the right place to post about PBEQ questions. I am using PBEQ to calculate pka of amino acids in a protein. In the script I downloaded from Roux Lab, there is a statement for the use of Atomic Born Radii and is as follows;

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prnlev 0
stream radius.str
prnlev 5
scalar wmain statistics select .not. type H* end
define check select (.not type H* ) .and. ( property wmain .eq. 0.0 ) show end
if ?nsel ne 0 stop !some heavy atom have a zero radius

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The program runs fine till here, but stops with the following error.

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PBEQ> prnlev 0

***** LEVEL 0 WARNING FROM <SELRPN> *****
***** No VDW parameters available for CHEM token
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

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Please explain what can be the reasons. Are there any VdW parameters it is not able to find in the PARAMETER file I read in the beginning of the script? All comments will be great and in fact I am a bit newbie to these sort of calculations.

Thanks in advance,

Vivek