From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Oct 18 2018 - 15:10:31 CDT
It looks like you are following the alchemical tutorial. You need to
download the tutorial files, particularly the Tcl file fep.tcl, which
defines the runFEP proc. This should be described in the text of the
tutorial.
On Thu, Oct 18, 2018 at 5:13 AM soroush ziaei <soroush.ziaei7337_at_gmail.com>
wrote:
> dear brian, thank you very much for your answer.
> i have solved errors that i mentioned above but after that an error
> implicitly says:
> ( eq2.log: )
>
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR: runFEP
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>
> now, what should i do?!
> please help, i'm in a hurry.
>
>
>
>
>
> On Wed, Oct 17, 2018 at 5:46 PM Brian Radak <brian.radak_at_gmail.com> wrote:
>
>> This is an incredibly explicit error message -- what more would you like
>> it say? You make reference to keywords that don't exist (they are all
>> enumerated, starting with "lambda2") and have neglected required keywords,
>> starting with "cutoff".
>>
>> It seems like you should look at one of the introductory tutorials before
>> attempting an advanced protocol like alchemical calculations.
>>
>> BKR
>>
>> ---------- Forwarded message ---------
>> From: soroush ziaei <soroush.ziaei7337_at_gmail.com>
>> Date: Wed, Oct 17, 2018 at 5:10 AM
>> Subject: Re: namd-l: the fep error in third part of config file
>> To: Brian Radak <brian.radak_at_gmail.com>
>>
>>
>> my pdb file or zero.fep containes:
>>
>> CRYST1 36.000 36.000 36.000 90.00 90.00 90.00 P 1
>> 1
>> ATOM 1 N2 N X 1 -0.935 -1.034 -0.000
>> 1.00300.00 N
>> ATOM 2 C1 C X 1 -1.457 0.278 0.000
>> 1.00300.00 C
>> ATOM 3 N1 N X 1 -0.451 1.264 0.000
>> 1.00300.00 N
>> ATOM 4 C2 C X 1 0.970 1.091 0.000
>> 1.00300.00 C
>> ATOM 5 C3 C X 1 1.345 -0.323 0.000
>> 1.00300.00 C
>> ATOM 6 C4 C X 1 0.431 -1.327 0.000
>> 1.00300.00 C
>> ATOM 7 O1 O X 1 -2.686 0.522 -0.000
>> 1.00300.00 O
>> ATOM 8 O2 O X 1 1.750 2.072 -0.000
>> 1.00300.00 O
>> ATOM 9 F1 F X 1 2.715 -0.624 -0.000
>> 1.00300.00 F
>> ATOM 10 H1 H X 1 -1.622 -1.780 -0.000
>> 1.00300.00 H
>> ATOM 11 H2 H X 1 -0.777 2.230 -0.000
>> 1.00300.00 H
>> ATOM 12 H3 H X 1 0.717 -2.373 -0.000
>> 1.00300.00 H
>> ATOM 13 OH2 TIP3W 5 -14.332 -7.918 -2.096 1.00 0.00
>> WT1 O
>> ATOM 14 H1 TIP3W 5 -14.776 -7.549 -2.899 1.00 0.00
>> WT1 H
>>
>>
>> and my eq2.log containes:
>>
>> # error 1:
>>
>> ERROR: 'cutoff' is a required configuration option
>> ERROR: cutoff defines: local electrostatic and Vdw distance
>> ERROR: 'exclude' is a required configuration option
>> ERROR: exclude defines: Electrostatic and VDW exclusion policy
>> ERROR: The following variables were set in the
>> ERROR: configuration file but are NOT VALID
>> ERROR: lambda2
>> ERROR: lambda
>> ERROR: dlambda
>> ERROR: fepEquilSteps
>> ERROR: fepOutFreq
>> ERROR: fepOutFile
>> ERROR: fepCol
>> ERROR: fepfile
>> ERROR: fep
>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>
>>
>>
>>
>>
>>
>> # error 2:
>>
>> ERROR: 'alchLambda' is a required configuration option
>> ERROR: when 'alch' is set
>> ERROR: alchLambda defines: Coupling parameter value
>> ERROR: 'alchLambda2' is a required configuration option
>> ERROR: when 'alch' is set
>> ERROR: alchLambda2 defines: Coupling comparison value
>> Warning: The following variables were set in the
>> Warning: configuration file but will be ignored:
>> Warning: fixedAtomsForces (fixedatoms)
>> Warning: fixedAtomsFile (fixedatoms)
>> Warning: fixedAtomsCol (fixedatoms)
>> ERROR: The following variables were set in the
>> ERROR: configuration file but are NOT VALID
>> ERROR: runFEP
>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>
>> what should i do? please help, thanks.
>>
>> best regard, soroush
>>
>> On Mon, Oct 15, 2018 at 10:47 PM Brian Radak <brian.radak_at_gmail.com>
>> wrote:
>>
>>> It would really help if you posted the exact error message.
>>>
>>> Based on your input alone, it would appear that you have used invalid
>>> keywords. "lambda" and "lambda2" should probably be "alchLambda" and
>>> "alchLambda2". I don't know what you mean by "dlambda" as there is no such
>>> keyword in the manual.
>>>
>>> I also suspect that your for-loop will fail since alchLambda and
>>> alchLambda2 must both be between 0 and 1.
>>>
>>> HTH,
>>> BKR
>>>
>>>
>>>
>>>
>>> On Mon, Oct 15, 2018 at 10:51 AM soroush ziaei <
>>> soroush.ziaei7337_at_gmail.com> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I want to calculate fep in namd but when I run this simulation, an
>>>> fatal error appears in the terminal about configuration file. I puted some
>>>> parameters here:
>>>>
>>>> [Note: the first conf file is about minimization and the second one is
>>>> related to increasing temperature and the last one that is loaded below]
>>>>
>>>> I think the problem is about rand.fep (pdb) as input for fep, right?
>>>>
>>>> i'll be happy, if someone help me.
>>>>
>>>>
>>>>
>>>> Best regard, soroush
>>>>
>>>>
>>>>
>>>> # NAMD config file
>>>>
>>>> numsteps 15000000
>>>>
>>>> structure solvate.psf
>>>>
>>>> coordinates solvate.pdb
>>>>
>>>> outputName eq2
>>>>
>>>> XSTfile eq2.xst
>>>>
>>>>
>>>>
>>>> bincoordinates eq1.coor
>>>>
>>>> binvelocities eq1.vel
>>>>
>>>> extendedSystem eq1.xsc
>>>>
>>>>
>>>>
>>>> langevin on
>>>>
>>>> langevinDamping 3
>>>>
>>>> langevinTemp 310
>>>>
>>>> langevinHydrogen on
>>>>
>>>>
>>>>
>>>> useGroupPressure yes
>>>>
>>>> useFlexibleCell no
>>>>
>>>> useConstantArea no
>>>>
>>>>
>>>>
>>>> langevinPiston on
>>>>
>>>> langevinPistonTarget 1
>>>>
>>>> langevinPistonPeriod 100
>>>>
>>>> langevinPistonDecay 50
>>>>
>>>> langevinPistonTemp 310
>>>>
>>>>
>>>>
>>>> fep on
>>>>
>>>> fepfile rand.fep
>>>>
>>>> fepCol B
>>>>
>>>> fepOutFile rand.fepout
>>>>
>>>> fepOutFreq 5
>>>>
>>>> fepEquilSteps 3200
>>>>
>>>>
>>>>
>>>> set step 0
>>>>
>>>> set dstep 0.025
>>>>
>>>> dlambda $dstep
>>>>
>>>>
>>>>
>>>> while {$step < 1} {
>>>>
>>>> firsttimestep 0
>>>>
>>>> lambda $step
>>>>
>>>> set step [expr $step+$dstep]
>>>>
>>>> lambda2 $step
>>>>
>>>> run 6400
>>>>
>>>> }
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> switching on
>>>>
>>>> switchDist 10
>>>>
>>>> cutoff 12
>>>>
>>>> pairlistdist 14
>>>>
>>>> margin 3
>>>>
>>>>
>>>>
>>>> binaryOutput yes
>>>>
>>>> binaryRestart yes
>>>>
>>>>
>>>>
>>>> parameters par file.par
>>>>
>>>> parameters par2.prm
>>>>
>>>> paraTypeCharmm on
>>>>
>>>> wrapAll yes
>>>>
>>>> wrapNearest yes
>>>>
>>>> COMmotion no
>>>>
>>>>
>>>>
>>>> outputEnergies 500
>>>>
>>>> outputTiming 500
>>>>
>>>> xstFreq 500
>>>>
>>>> dcdFreq 250
>>>>
>>>> restartFreq 500
>>>>
>>>>
>>>>
>>>> timestep 1
>>>>
>>>> nonBondedFreq 2
>>>>
>>>> fullElectFrequency 4
>>>>
>>>> stepsPerCycle 20
>>>>
>>>>
>>>>
>>>> Pme on
>>>>
>>>> PmeGridSizeX 40
>>>>
>>>> PmeGridSizeY 40
>>>>
>>>> PmeGridSizeZ 40
>>>>
>>>>
>>>>
>>>> exclude scaled1-4
>>>>
>>>> 1-4scaling 1
>>>>
>>>>
>>>>
>>>> if {1} {
>>>>
>>>> fixedAtoms off
>>>>
>>>> fixedAtomsFile fix.pdb
>>>>
>>>> fixedAtomsCol B
>>>>
>>>> fixedAtomsForces off
>>>>
>>>> }
>>>>
>>>>
>>>>
>>>> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
>>>> Windows 10
>>>>
>>>>
>>>>
>>>
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