Fwd: the fep error in third part of config file

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed Oct 17 2018 - 09:14:48 CDT

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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