On Wed, Apr 11, 2012, Elisa Frezza wrote:
>
> The input files are:
>
> run: MD
> &cntrl
> imin = 0, irest = 0 , ntx = 1,
> nstlim = 2500000, dt = 0.002,
> ntc = 2 , ntf = 2,
> ntt = 3, gamma_ln = 2.0,
> tempi = 298.0, temp0 =298.0,
> ntb = 1 ,
> ntpr = 250 , ntwx = 250, ntwr = 500 ,
> cut = 9,
> ig = -1
> ioutfm = 1
> nmropt=1,
> ntr=1
> /
> &ewald
> nfft1 = 90,
> nfft2 = 90,
> nfft3 = 90,
> /
> &wt type='DUMPFREQ', istep1=1, /
> &wt type='END' /
> DISANG=dist_chi.RST
> DUMPAVE=restraint.log
> LISTIN=POUT
> LISTOUT=POUT
> Keep DNA fixed with weak restraints
> 0.05
> RES 1 48
> END
> END
>
I don't see what is wrong. Can you try a quick run with sander rather than
pmemd? (Set nstlim=2, not 2500000!).
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
> 5. REFERENCE ATOM COORDINATES
> ----- READING GROUP 1; TITLE:
> DISANG=dist_chi.RST
Clearly, pmemd is trying to read the "DISANG" line as the title for the group
restraints, but I don't think it should be doing that. But I might be missing
something, which is why having a quick check with sander would help.
Note that you could avoid this whole issue of where the group input should be by
using restraint_wt and restraintmask in the &cntrl namelist. (But this was
only been implemented in pmemd in Amber11 and later: this is one of many
reasons to consider upgrading to Amber12.)
...thanks...dac
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Received on Thu Apr 12 2012 - 06:00:05 PDT
