AMBER Archive (2008)

Subject: Re: AMBER: RESTRAINTS: no valid redirection found

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Nov 17 2008 - 13:21:01 CST

I added the lacking flag, now the line for restraint in the in file reads

nmropt=1, ntr=1,

Now the positional restraints are read correctly. However, the out
file warns that:

  3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

 begin time read from input coords = 10.000 ps

           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
 TEMP0 0 600 290.000000 300.000000 0 0

 RESTRAINTS:
  No valid redirection requests found
                          ** No restraint defined **

                  Done reading weight changes/NMR restraints

 Number of triangulated 3-point waters found: 0
| Dynamic Memory, Types Used:
| Reals 771203
| Integers 1594280

If the flag "nmropt=1" is removed, that warning "No valid request .."
disappears, but the weight restraint on the temperature is not read.

Does this simply mean that there are nothing else to do about
"nmropt=1" (and the warning should be ignored) or is the procedure
wrongly started?

pmemd is used with mpirun

Thanks
francesco

On Mon, Nov 17, 2008 at 6:34 PM, Robert Duke <rduke_at_email.unc.edu> wrote:
> I don't see an ntr=1 in the &cntrl. - Bob Duke
> ----- Original Message ----- From: "Francesco Pietra"
> <chiendarret_at_gmail.com>
> To: "Amber" <amber_at_scripps.edu>
> Sent: Monday, November 17, 2008 12:15 PM
> Subject: AMBER: RESTRAINTS: no valid redirection found
>
>
>> With pmemd (i.e., I can't use restraintmask) in Amber10 the following
>> heat5.in file
>>
>> Heating gradually under GB conditions
>> with restraint on Cl-
>> Then continuing equilibration at 300K.
>> &cntrl
>> imin=0, irest=0, ntx=1, ntb=0,
>> igb=5, ntc=2, ntf=2,
>> ntt=3, gamma_ln=2.0,
>> nstlim=3000, dt=0.002,
>> ntpr=100, ntwx=100,
>> tempi=290.0, temp0=300.0,
>> cut=999.0, rgbmax=999.0,
>> nmropt=1
>> /
>> &wt TYPE='TEMP0', istep1=0, istep2=600,
>> value1=290.0, value2=300.0,
>> /
>> &wt TYPE='END'
>> /
>> Keep Cl- 427 restrained
>> 32.0
>> RES 427
>> END
>> END
>>
>> (actually there are several other C-, same layout)
>>
>> did not succeed in imposing positional restraints, as from the out file:
>>
>> begin time read from input coords = 10.000 ps
>>
>>
>>
>> Begin reading energy term weight changes/NMR restraints
>> WEIGHT CHANGES:
>> TEMP0 0 600 290.000000 300.000000 0 0
>>
>> RESTRAINTS:
>> No valid redirection requests found
>> ** No restraint defined **
>>
>> Done reading weight changes/NMR restraints
>>
>>
>> In previous procedure heat4.in (from which heat4.rst was used to
>> launch this procedure) there was no positional restraint. Does ""No
>> valid redirection" mean that positional restraint should be placed
>> before weigth restraint?
>>
>> Thanks
>>
>> francesco pietra
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