AMBER Archive (2008)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Nov 17 2008 - 13:58:18 CST

And it executes, right? Positional restraints are different than nmr
restraints; nmr restraints have to be defined with redirection files, and
you are not using them here; the code is just reporting that there are none,
since you are using nmropt .eq. 1 (which is required to use redirection
file-based nmr restraints). So you SHOULD be okay, I think (but am not
certain since I have not seen all your output). This stuff is convoluted
due to a lot of history; folks have been able to get pmemd to do what they
want, but I think there were some restrictions on how you specified the nmr
restraints. Since I never use nmr restraints, I am a little vague in this
area. We should probably move to a newer more sane mdin format, but then a
lot of old stuff wouldn't work. In s/w, you can have to live with old
decisions for a very long time...
Best Regards - Bob

----- Original Message -----
From: "Francesco Pietra" <chiendarret_at_gmail.com>
To: <amber_at_scripps.edu>
Sent: Monday, November 17, 2008 2:21 PM
Subject: Re: AMBER: RESTRAINTS: no valid redirection found

>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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