AMBER Archive (2005)

Subject: RE: AMBER: Error on restrained MD equilibration (AMBER 7)

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Wed Jun 01 2005 - 05:20:40 CDT

Hi Ross,

It seems the commas were all right. I could run either just restraints on
residue 1 (ntr=1 & nmropt=0) or just weight change on temperature restraint
(ntr=0 & nmropt=1). But I could not run both of them at the same time (ntr=1 &
nmropt=1), which gave the error message

   5. REFERENCE ATOM COORDINATES

    ----- READING GROUP 1; TITLE:
 MD heating from 0 to 300K with restraints on the solute

     rfree: Error decoding variable 1 3 from:
 &cntrl

There might be some conflicts between those two flags that I could not find out
now.

Lan

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

> Hi Lan,
>
> > equilibrate the solvent. Anything else we could consider?
>
> A few things you could try. First of all remove all the extra commas from
> the last item in each namelist - some compilers don't like this. Second
> specify the restraint force as 10.0 instead of 10 since it is a float. I.e.
>
> MD heating from 0 to 300K with restraints on the solute
> &cntrl
> imin = 0, ntpr = 100, ntwx = 100, ntwe = 100, ntwr = 1000,
> nstlim =10000, dt = 0.001,
> ntb = 1,cut = 8, ntr = 1, ntc = 2, ntf = 2, nmropt = 1,
> tempi = 0.0, temp0 = 300.0, ntt = 1, tautp = 0.5
> &end
> &wt
> type='TEMP0', istep1=0, istep2=500,
> value1=0.0, value2=300.0
> &end
> &wt
> type='TEMP0', istep1=500, istep2=20000,
> value1=300.0, value2=300.0
> &end
> &wt
> type='END'
> &end
> Group input for restraint atoms
> 10.0
> RES 1 1
> END
> END
>
> If that doesn't work try it out without the weight change info and see if
> you can get it to work with just the restraints, as a test.
>
> All the best
> Ross
>
>
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
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