colvin wrote:
> K is the potassium ion in the system and in the topology file used, it is
> clearly stated:
>
> MASS 8 POT 39.09830 K ! Potassium Ion
>
>
> But i do not know why it cannot map symbol K. Pls assist.
>
Dear Colvin,
If you look at an example charmm topology file in
$AMBERHOME/dat/chamber/top_all22_prot.inp and specifically, a random
region of the MASS section:
MASS 20 C 12.01100 C ! carbonyl C, peptide backbone
MASS 21 CA 12.01100 C ! aromatic C
MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH
MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2
MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3
MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons
MASS 26 CPH2 12.01100 C ! his CE1 carbon
MASS 27 CPT 12.01100 C ! trp C between rings
MASS 28 CY 12.01100 C ! TRP C in pyrrole ring
MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA)
MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG)
MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD)
Juxtaposing your example line:
MASS 8 POT 39.09830 K ! Potassium Ion
It seems not to be the same format as above, i.e. the floating point
number field is one space to the left. Can you correct this and see if
this fixes the issue?
Regards,
Mark
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Received on Wed Mar 02 2011 - 08:30:05 PST
