Dear All CHARMMer,

I want to use shake to constrain my protein structure. So I have two questions.

1) During MD calculation, I would like to fix the shape of helix and sheet to save time, but I hope the distance between different helix and sheet would change in MD calculation. I don't know if it is appropriate to use Shak Angh. Accually after I looked for the mannual of CHARMM, I choose this. Could anybody give me any suggestion about that?

2) I have started to use shak, but the calculation stopped abnormally, the output is as following:

CHARMM> shak angh sele atom ctf_ 2 * end

SELRPN> 20 atoms have been selected out of 1004

SHKCOM> SHAKE parameters: TOL = 0.1000D-09 MXITer = 500

SHKSET: * WARNING * Atom 18 is involved in:

4 bond end, 3 angle mid, and 3 angle end constraints.

The number of degrees of freedom will probably be wrong.

SHKSET: * WARNING * Atom 25 is involved in:

3 bond end, 0 angle mid, and 4 angle end constraints.

The number of degrees of freedom will probably be wrong.

39 constraints will held by SHAKE.

***** ERROR IN SHAKEA ***** COORDINATE RESETTING WAS NOT ACCOMPLISHED IN 500 ITERATIONS

*** LEVEL -2 WARNING *** BOMLEV IS -5

SHAKEA: Using routine SHAKEA2 for shake calculation.

contraints: 39

EBONDC: Using routine EBONDFS for energy calculation.

EANGLC: Using routine EANGLFS for energy calculation.

EBONDC: Using routine EBONDFS for energy calculation.

EPHIC: Using routine EPHIFS for energy calculation.

EIMPHIC: Using routine EIPHIFS for energy calculation.

ENBOND: Using routine ENBFS8 for energy calculation.

***** ERROR IN SHAKEF ***** FORCE RESETTING WAS NOT ACCOMPLISHED IN 500 ITERATIONS

*** LEVEL -2 WARNING *** BOMLEV IS -5

***** ERROR IN SHAKEA ***** COORDINATE RESETTING WAS NOT ACCOMPLISHED IN 500 ITERATIONS

*** LEVEL -2 WARNING *** BOMLEV IS -5

SHAKEA: Using routine SHAKEA2 for shake calculation.

contraints: 39

EBONDC: Using routine EBONDFS for energy calculation.

EANGLC: Using routine EANGLFS for energy calculation.

EBONDC: Using routine EBONDFS for energy calculation.

EPHIC: Using routine EPHIFS for energy calculation.

EIMPHIC: Using routine EIPHIFS for energy calculation.

ENBOND: Using routine ENBFS8 for energy calculation.

***** ERROR IN SHAKEF ***** FORCE RESETTING WAS NOT ACCOMPLISHED IN 500 ITERATIONS

What is wrong with calculation?

I am looking forward to your answer.

Thank you very much

Holly