Hi Sophia:
OK, I went back and checked. There are four variables that apparently
did not make their way into Sander_PME, although I believe at least
some of them were in the pre-release version of Sander_PME about which
the sander/pme Interface stuff was designed.
At any rate, I have removed those variables from the appropriate Sander
".def" script (sander_pme_namelist.def). You should place this file (attached) in the
amber6/src/interface/def directory (replacing the version already there),
then "recompile" the amber interface (not the interface program, but the
script). I believe this should take care of all the "not in namelist"
problems.
dap
Sophia Kondratova wrote:
>
> Thanks for the reply.
>
> I did what you told me, and interface does make a different .inp file but
> still there is something wrong with the variables, because the output that I
> get is:
> ...
> Warning: IPRR set but ignored by Sander_PME
> Warning: IPRW set but ignored by Sander_PME
> No coordinate archive file written
> No velocity archive file written
> No energy archive file written
> No position restraints (default)
> No CAP will be used.
> namelist read: variable not in namelist
> apparent state: unit 5 named min2.inp
> last format: list io
> lately reading sequential formatted external IO
>
> Maybe there is something wrong with my sander_pme_namelist.def file.
>
> Any help would be appreciated
>
> >===== Original Message From David Pearlman <dap_at_vpharm.com> =====
> >Howdy:
> >
> >First thing you need to do is use the command
> >
> > sander/pme
> >
> >rather than just the command
> > sander
> >
> >This will use the namelist variables that are appropriate for
> >sander_pme. Using simply the "sander" command is appropriate
> >for using sander_classic.
> >
> >dap
> >
> >
> >Sophia Kondratova wrote:
> >>
> >> Hello,
> >>
> >> I am trying to use interface to do some examples posted on the web,
> >> particularly the methane min, md and the input file that interface
> generates
> >> cannot be read by sander, because it complains that there are some missing
> >> variables.
> >>
> >> namelist read: variable not in namelist
> >> apparent state: unit 5 named min1.inp
> >> last format: list io
> >> lately reading sequential formatted external IO
> >>
> >> However, when I use sander_classic, the min and md seems to run. I have
> >> amber6, so therefore I would assume that I would have the latest version of
> >> interface that would properly convert the interface input file to a file
> that
> >> sander could read as well as sander_classic. Maybe there is a file I am
> >> missing or I have to go and change something in one of the .def file that
> >> define the variables that interface should put in.
> >>
> >> Any help would be appreciated
> >>
> >> Sophia Kondratova
> >> Chemistry Graduate Student
> >> University of New Brunswick
> >> Fredericton, Canada
>
> Sophia Kondratova
> Chemistry Graduate Student
> University of New Brunswick
> Fredericton, Canada<x-html>
! interface code to write namelist formatted Interface input for Sander_pme
! D.A. Pearlman , 3/99
!
! The following variables, which were included in the Amber 5.0 &cntrl
! namelist, are not in the Amber6/sander_pme namelist:
! KFORM ICHDNA IPRR IPRW TAUTS ISOLVP IFTRES NRUN INIT NATRCM
! IDIEL IMGSLT NTNB NTID ISFTRP RWELL XON XOFF TAUV TAUV0
! VZERO CUT2ND IEWALD COSMOD ITRSLU NTWR ILBOPT ILBNOB LBFREQ LBVERB
! LBWGHT
!
! The following variables, which are in the &cntrl namelist for
! Amber6/sander_pme were not in the Amber50 namelist:
! IALTDIST IGB IGBFREQ
! writes two namelists:
! 1) &cntrl (main variables list)
! 2) &ewald (Ewald control list)
! redefine FORMEC to output 7 sig digits to namelist
define FORMEC = "G16.7"
assign nmfmtuse = "(10(t5,a,t28,', ',:,a,t53,', ',:,a,t78,',',:,/))"
write ("TITLE: <TITLE>" ) \
/outfile = outfil \
/out_form = (a,/)
write(" &cntrl") /outfile=outfil/out_form=(a)
write ("timlim = <TIMLIM>","irest = <IREST>" ,"ibelly = <IBELLY>", \
"imin = <IMIN>", \
"ipol = <IPOL>" ) \
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("ntx = <NTX>" ,"ntxo = <NTXO>" ,"ntcx = <NTCX>", \
"ig = <IG>" ,"tempi = <TEMPI>" ,"heat = <HEAT>") \
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("ntb = <NTB>" ) \
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ( "ntt = <NTT>" ,"temp0 = <TEMP0>", \
"dtemp = <DTEMP>" ,"tautp = <TAUTP>" , \
"vlimit = <VLIMIT>") \
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("ntp = <NTP>" ,"pres0 = <PRES0>" ,"comp = <COMP>", \
"taup = <TAUP>" ,"npscal = <NPSCAL>")\
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("ndfmin = <NDFMIN>","ntcm = <NTCM>" ,"nscm = <NSCM>")\
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("nstlim = <NSTLIM>", "ntu = <NTU>",\
"t = <T>" ,"dt = <DT>" ) \
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("ntc = <NTC>" ,"ntcc = <NTCC>" ,"nconp = <NCONP>",\
"tol = <TOL>" ,"jfastw = <JFASTW>")\
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("ntf = <NTF>" ,"ntn = <NTN>" , \
"nsnb = <NSNB>" )\
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("cut = <CUT>" ,"scnb = <SCNB>" ,"scee = <SCEE>",\
"dielc = <DIELC>") \
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("ntpr = <NTPR>" ,"ntwx = <NTWX>" ,"ntwv = <NTWV>",\
"ntwe = <NTWE>" , \
"ntpp = <NTPP>" ,"ioutfm = <IOUTFM>",\
"ntwprt = <NTWPRT>","ntwpr0 = <NTWPR0>") \
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("ntr = <NTR>" ,"nrc = <NRC>" ,"ntrx = <NTRX>",\
"taur = <TAUR>" ,"nmropt = <NMROPT>", \
"pencut = <PENCUT>" )\
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("ivcap = <IVCAP>" ,"fcap = <FCAP>")\
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("maxcyc = <MAXCYC>","ncyc = <NCYC>" ,"ntmin = <NTMIN>",\
"dx0 = <DX0>" ,"dxm = <DXM>" ,"dele = <DELE>",\
"drms = <DRMS>")\
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
write ("igb = <IGB>" ,"igbfreq= <IGBFREQ>" ) \
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
! new water name definition if defined:
if (jfastw.eq.1 .or. jfastw.eq.3) then
write ("watnam = '<WATNAM>'","owtnm = '<OWTNM>'" , \
"hwtnm1 = '<HWTNM1>'","hwtnm2 = '<HWTNM2>'") \
/outfile = outfil \
/out_form = <nmfmtuse>
echo /outfile=outfil
end if
!
! First, if nmropt=2 or 3, write the additional cards needed for volume
! and chemical shift restraint (lines 15A, 15B):
if (nmropt.eq.2 .or. nmropt.eq.3) then
write ("iscale = <ISCALE>","noeskp = <NOESKP>","ipnlty = <IPNLTY>",\
"maxsub = <MAXSUB>","scalm = <SCALM>" ,"tausw = <TAUSW>")\
/outfile=outfil\
/out_form=<nmfmtuse>
echo /outfile=outfil
end if
! Following variables not in distributed version
! write ("boxx(1)= <BOX1>", "boxx(2)= <BOX2>" ,"boxx(3)= <BOX3>" ,\
! "betar = <BETA>") \
! /outfile=outfil\
! /out_form=<nmfmtuse>
! Write out any additional namelist variables specified by the using
! using the "nameset" command.
if (iasval("inml_add").eq.0) assign inml_add = 0
if (inml_add.gt.0) then
do i = 1,inml_add,3
if (inml_add.ge.i+2) then
write ("<addnml> = <<addnml>>" , \
"<addnml<i+1>> = <<addnml<i+1>>>", \
"<addnml<i+2>> = <<addnml<i+2>>>") \
/outfile=outfil\
/out_form=<nmfmtuse>
else if (inml_add.eq.i+1) then
write ("<addnml> = <<addnml>>" , \
"<addnml<i+1>> = <<addnml<i+1>>>") \
/outfile=outfil\
/out_form=<nmfmtuse>
else
write ("<addnml> = <<addnml>>" ) \
/outfile=outfil\
/out_form=<nmfmtuse>
end if
end do
echo /outfile=outfil
end if
write(" &end") /outfile=outfil/out_form=(a)
! write out &ewald namelist if the ewald command was specified (iewald=1)
if (iewald.ne.1) goto ewaldskip
write(" ") /outfile=outfil/out_form=(a)
write(" &ewald") /outfile=outfil/out_form=(a)
! only output cell parameters if they were specified
if (iasval("A_EW").ne.0) \
write ("a = <A_EW>" ,"b = <B_EW>" ,"c = <C_EW>" ,\
"alpha = <ALP_EW>" ,"beta = <BET_EW>" ,"gamma = <GAM_EW>") \
/outfile=outfil\
/out_form=<nmfmtuse>
write ("nfft1 = <NFFT1>" ,"nfft2 = <NFFT2>" ,"nfft3 = <NFFT3>" ,\
"order = <ORDER_EW>","ischrgd = <ischrgd_ew>" ,\
"verbose= <VERBOSE_EW>" ,"ew_type= <CHECKACC_EW>" ,\
"dsum_tol= <DSUM_TOL_EW>")\
/outfile=outfil\
/out_form=<nmfmtuse>
write ("ew_coeff= <EW_COEFF>" ,"nbflag = <NBFLAG>" ,"skinnb = <SKINNB>" ,\
"nbtell = <NBTELL>" ,"netfrc = <NETFRC>" ,"frc_int= <FRC_INT>" ,\
"ee_type = <EE_TYPE>" ,\
"vdwmeth= <VDWMETH>" ,"eedmeth= <EEDMETH>" ,\
"eedtbdns = <EEDTBDNS>" ) \
/outfile=outfil\
/out_form=<nmfmtuse>
! Write out any additional namelist variables specified by the using
! using the "nameset/ewald" command.
if (iasval("inml_add_ewald").eq.0) assign inml_add_ewald = 0
if (inml_add_ewald.gt.0) then
do i = 1,inml_add_ewald,3
if (inml_add_ewald.ge.i+2) then
write ("<addnml_ewald> = <<addnml_ewald>>" , \
"<addnml_ewald<i+1>> = <<addnml_ewald<i+1>>>", \
"<addnml_ewald<i+2>> = <<addnml_ewald<i+2>>>") \
/outfile=outfil\
/out_form=<nmfmtuse>
else if (inml_add.eq.i+1) then
write ("<addnml_ewald> = <<addnml_ewald>>" , \
"<addnml_ewald<i+1>> = <<addnml_ewald<i+1>>>") \
/outfile=outfil\
/out_form=<nmfmtuse>
else
write ("<addnml_ewald> = <<addnml_ewald>>" ) \
/outfile=outfil\
/out_form=<nmfmtuse>
end if
end do
echo /outfile=outfil
end if
echo /outfile=outfil
write(" &end") /outfile=outfil/out_form=(a)
ewaldskip:
! reset FORMEC to default of 16.5
define FORMEC = "G16.5"
</x-html>
Received on Tue Oct 30 2001 - 12:13:42 PST