From: soroush ziaei (soroush.ziaei7337_at_gmail.com)
Date: Thu Oct 18 2018 - 04:13:08 CDT
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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