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
>
> _______________________________________________
> 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
Received on Sat Jun 11 2011 - 03:00:03 PDT
