Hi,
nope, it didn't solve the problem. However, in CHARMM-GUI, they have other
options of ion, so i change it to NaCl and now chamber can read and write
out amber prmtop & inpcrd.
Thanks and regards,
Colvin
On Thu, Mar 3, 2011 at 12:18 AM, Mark Williamson <mjw.mjw.name> wrote:
> 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 Thu Mar 03 2011 - 01:30:04 PST
