Dear Dr. Thomas Steinbrecher
Thanks for your attention
You are right. DG9 and DC18 really are not my residue names.
Thus, since DG and DC are not unique in dna, I useed crgmask =
(:9.O6,H1,N2,H21,H22
| :18.N4,H41,H42,H5).
unfortunately, run was stopped. there is error in reading namelist cntrl at
the end of out file.
Can I use atom number rather than atom name? crgmask =
'.269,271,273,274,275,553,555,556,557'. is it true?
please help me to resolve this problem.
On Tue, Feb 7, 2012 at 2:06 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > crgmask = "DG9.O6,H1,N2,H21,H22 DC18.N4,H41,H42,H5"
>
> you can't write the crgmask like this. There is a specific format for
> writing these masks, Appendix C of the Amber manual has a few examples.
>
> In your case, it would probably look something like this:
>
> (:DG9.O6,H1,N2,H21,H22 | :DC18.N4,H41,H42,H5)
>
> if DG9 and DC18 really are your residue names, which I doubt. You can most
> likely just give the residue numbers :9 and :18, *or* the names :DG and
> :DC if they are unique (which they normally are not in DNA).
>
> Be careful, since sander will run with any valid chargemask. I think the
> output lists all atoms that have their charge stripped, so double-check
> these.
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Tue Feb 07 2012 - 04:30:03 PST
