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
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Received on Sat Jun 11 2011 - 02:30:03 PDT
