Hello sir,
There is no file in leap directory ended with .log or .out, here is the list of files which were found in leap
[root.nis leap]# ls0README ff91_prm.cmd ff94_iowatprm.cmd ions94.cmd plepff91 ff94 ff94_prm.cmd lib91.cmd Run.tleapff91.cmd ff94.cmd ions91.cmd lib94.cmd tleap
regards,
Souvik Sur
Ph. D. Student
Department Of Chemistry
University Of Delhi
India
> Date: Sat, 11 Jun 2011 17:32:24 +0800
> From: teonghan.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Loadin AMBER9 in linux
>
> Hi,
>
> The files you post here are not ended with either .log or .out. Can you
> check again?
>
> Thanks.
>
> On Sat, Jun 11, 2011 at 5:23 PM, souvik sur <souviksur.hotmail.com> wrote:
>
> >
> > Hello sir,
> > I have found these following files in leap:
> > [souvik.nis leap]$ vi ff91_prm.cmd
> >
> > logfile ff91_prm.log
> >
> >
> >
> > set default OldPrmtopFormat on
> >
> > source oldff/leaprc.ff91
> >
> >
> >
> > logfile ff91_prm.log
> >
> >
> >
> > x = loadpdb ff91/all_aminoan.p
> >
> > saveamberparm x ./all_aminoan91.top ./all_aminoan91.crd
> >
> >
> >
> > ncres = { NALA CALA NPRO CPRO }
> >
> > x = loadpdbusingseq ff91/all_aminonc.p ncres
> >
> > saveamberparm x ./all_aminonc91.top ./all_aminonc91.crd
> >
> >
> >
> > strand = { HB RADE RPOM RURA RPOM RCYT RPOM RGUA HE }
> >
> > x = loadpdbusingseq ff91/all_rna91.p strand
> >
> > # adjust charges of terminal residues
> >
> > set x.2.O5' charge -0.425
> >
> > set x.8.O3' charge -0.514
> >
> >
> >
> > #set x.2.O5' type OH
> >
> > #set x.8.O3' type OH
> >
> >
> >
> > "ff91_prm.cmd" [readonly] 32L, 808C
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > [souvik.nis leap]$ vi ff94_iowatprm.cmd
> >
> > logfile ff94_iowatprm.log
> >
> >
> >
> > set default OldPrmtopFormat on
> >
> > source ../../dat/leap/cmd/leaprc
> >
> >
> >
> > logfile ff94_iowatprm.log
> >
> >
> >
> > #
> >
> > # add ions in
> > vacuum --test alias too (ai==addions)
> >
> > #
> >
> > x = loadpdb ff94/all_dna94.p
> >
> > ai x IB 0
> >
> > saveamberparm x ./all_dnaio94.top ./all_dnaio94.crd
> >
> >
> >
> > #
> >
> > # just solvate
> >
> > #
> >
> > x = loadpdb ff94/all_dna94.p
> >
> > alignaxes x
> >
> > solvatebox x WATBOX216 10
> >
> > saveamberparm x ./all_dnawat94.top ./all_dnawat94.crd
> >
> >
> >
> > "ff94_iowatprm.cmd" [readonly] 41L, 748C 1,1
> > Top
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > [souvik.nis leap]$ vi ions94.cmd
> >
> > clearVariables
> >
> > logFile ions94.log
> >
> > #
> >
> > # Monovalent,
> > monoatomic ions using '94 atom types.
> >
> > # The Li+..Cs+
> > series uses types derived from the
> >
> > # work of Aqvist
> > (see force field documentation).
> >
> > # IB (ion+water)
> > is a hack for vacuum modeling.
> >
> > #
> >
> >
> >
> > i = createAtom
> > Li+ Li 1.0
> >
> > set i element Li
> >
> > set i position { 0
> > 0 0 }
> >
> > r = createResidue Li+
> >
> > add r i
> >
> > Li+ = createUnit Li+
> >
> > add Li+ r
> >
> > saveOff Li+ ./ions94.lib
> >
> >
> >
> > i = createAtom
> > Na+ IP 1.0
> >
> > set i element Na
> >
> > set i position { 0
> > 0 0 }
> >
> > r = createResidue CIO
> >
> > add r I "ions94.cmd" [readonly] 90L, 1717C 1,1
> > Top
> >
> > [souvik.nis leap]$ vi ions91.cmd
> >
> > clearVariables
> >
> > logFile ions91.log
> >
> > #
> >
> > # Monovalent,
> > monoatomic ions using '91 atom types.
> >
> > # The Li+..Cs+
> > series uses types derived from the
> >
> > # work of Aqvist
> > (see force field documentation),
> >
> > # while IB is a
> > 'fat ion w/ waters' for vacuum use.
> >
> > #
> >
> >
> >
> > i = createAtom
> > Li+ QL 1.0
> >
> > set i element Li
> >
> > set i position { 0
> > 0 0 }
> >
> > r = createResidue Li+
> >
> > add r i
> >
> > Li+ = createUnit Li+
> >
> > add Li+ r
> >
> > saveOff Li+ ./ions91.lib
> >
> >
> >
> > i = createAtom
> > Na+ QN 1.0
> >
> > set i element Na
> >
> > set i position { 0
> > 0 0 }
> >
> > r = createResidue Na+
> >
> > add r i
> >
> > "ions91.cmd" [readonly] 74L, 1394C 1,1
> > Top
> >
> >
> >
> >
> >
> > regards,Souvik Sur
> > Ph. D. Student
> > Department Of Chemistry
> > University Of Delhi
> > India
> >
> >
> >
> >
> > > Date: Fri, 10 Jun 2011 22:07:39 +0800
> > > From: teonghan.gmail.com
> > > To: amber.ambermd.org
> > > Subject: Re: [AMBER] Loadin AMBER9 in linux
> > >
> > > Hi,
> > >
> > > Please look at the AmberTools/test/leap again and also all the subfolders
> > > inside. Examine all the files ended with either .log or .out. There
> > should
> > > be error reported inside one of those files. After that you can post here
> > > about the error.
> > >
> > > Thanks.
> > >
> > > On Fri, Jun 10, 2011 at 7:47 PM, souvik sur <souviksur.hotmail.com>
> > wrote:
> > >
> > > >
> > > > Hello sir,
> > > > There is no file named as ff94_prm.out, I found ff94_prm.cmd, and
> > inside of
> > > > the file I found:
> > > > [root.nis leap]# vi ff94_prm.cmdlogfile ff94_prm.log
> > > > set default OldPrmtopFormat onsource oldff/leaprc.ff94
> > > > logfile ff94_prm.log
> > > > x = loadpdb ff94/all_aminoan.psaveamberparm x ./all_aminoan94.top
> > > > ./all_aminoan94.crd
> > > > ncres = { NALA CALA NPRO CPRO }x = loadpdbusingseq ff94/all_aminonc.p
> > > > ncressaveamberparm x ./all_aminonc94.top ./all_aminonc94.crd
> > > > x = loadpdb ff94/all_dna94.psaveamberparm x ./all_dna94.top
> > > > ./all_dna94.crdstrand = { RC5 RG RU RA3 }x = loadpdbusingseq
> > > > ff94/all_rna94.p strandsaveamberparm x ./all_rna94.top ./all_rna94.crd
> > > > quit~~Type :quit<Enter> to exit Vim
> > > >
> > > > regards,
> > > > Souvik Sur
> > > > Ph. D. Student
> > > > Department Of Chemistry
> > > > University Of Delhi
> > > > India
> > > >
> > > >
> > > >
> > > >
> > > > > Date: Fri, 10 Jun 2011 06:08:45 -0400
> > > > > From: case.biomaps.rutgers.edu
> > > > > To: amber.ambermd.org
> > > > > Subject: Re: [AMBER] Loadin AMBER9 in linux
> > > > >
> > > > > On Fri, Jun 10, 2011, souvik sur wrote:
> > > > > >
> > > > > > yes sir, i got the file location but from that directory i am not
> > able
> > > > > > to run test/ff94_prm.out, it showed :
> > > > >
> > > > > We don't want you to *run* that file; it is not an excecutable file.
> > We
> > > > want
> > > > > to know the contents of the file. Maybe you have a friend who is
> > more
> > > > > familiar with computers who can help out(?)
> > > > >
> > > > > ....dac
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Regards,
> > > THChew
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Regards,
> THChew
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Received on Sat Jun 11 2011 - 05:00:02 PDT
