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#603 11/28/03 10:02 PM
Joined: Oct 2003
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cao Offline OP
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Dear all,

I was trying to calculate the volume of a protein, I used the following codes:

scalar wmain = radius
scalar wmain mult 0.85
scalar wmain add 1.4

coor volume space 660000 select segid prot end
set MV = ?volume

But, I got the following errors:

***** LEVEL -1 WARNING FROM *****
***** MUST FILL SCALAR ARRAYS TO USE
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

CHARMM> set MV = ?volume
RDCMND: can not substitute energy "?VOLUME"
Parameter: MV <- "?VOLUME"

Since I can't find any help in corman.doc, could anybody please help me fix it?
Thanks in advance!

cao #604 11/28/03 11:02 PM
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rmv Online Content
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The answer is both in corman.doc and in scalar.doc; in the description for COOR VOLUme, the phrase

"The SCALAR storage arrays must be filled before using this command. The first storage array [1] must contain the radii of each atom (RMIN) and the second storage array must contain the outer probe distance (RMAX) for each atom."

implies a couple additional SCALAR commands are needed. Try the following:

scalar wmain = radius
scalar wmain mult 0.85
scalar wmain store 1
scalar wmain add 1.4
scalar wmain store 2

coor volume space 660000 select segid prot end


Rick Venable
computational chemist

rmv #605 11/29/03 04:47 AM
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cao Offline OP
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Thank you very much!
I works now.


Moderated by  lennart, rmv 

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