Hi Lili,
yes it`s correct if you want use the restrain module in the min1.in you must
specify the residues that you want restraint, normally i use the minstep1 to
relax water and i restrain all the organic, the minstep2 is without restraint
(ntr=0) and all the system it`s free to relax.
Davide
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>Date: Tue, 17 Jul 2007 11:35:06 -0700
>From: "Lili Peng" <lilipeng.gmail.com>
>To: amber.scripps.edu
>Subject: Re: AMBER: refc error
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>Hi Davide,
>
>I used that line you suggested, but I get this error message:
>
>$AMBERHOME/exe/sander.1cpu -O -i min1.in -o min1.out -p taxol.prmtop -c
>taxol.inpcrd -r min1.rst -ref taxol.inpcrd
>forrtl: severe (24): end-of-file during read, unit 5, file
>/users/lpeng/min1.in
>Image PC Routine Line
>Source
>
>sander.1cpu 40000000011E3F70 Unknown Unknown Unknown
>sander.1cpu 40000000011DF0D0 Unknown Unknown Unknown
>sander.1cpu 4000000001166950 Unknown Unknown Unknown
>sander.1cpu 40000000010BDDA0 Unknown Unknown Unknown
>sander.1cpu 40000000010BD370 Unknown Unknown Unknown
>sander.1cpu 40000000010FDC80 Unknown Unknown Unknown
>sander.1cpu 40000000002DB910 Unknown Unknown Unknown
>sander.1cpu 40000000001C49E0 Unknown Unknown Unknown
>sander.1cpu 4000000000184D10 Unknown Unknown Unknown
>sander.1cpu 40000000001804F0 Unknown Unknown Unknown
>sander.1cpu 4000000000000490 Unknown Unknown Unknown
>sander.1cpu 4000000001207750 Unknown Unknown Unknown
>sander.1cpu 4000000000000300 Unknown Unknown Unknown
>
>Regarding David Case's email, could this problem be attributed to using
>restraintmask instead of ibelly?
>
>Thanks again,
>Lili
>
>On 7/16/07, Davide Moiani <moiani.scripps.edu> wrote:
>>
>> Hi Lili,
>>
>> sorry but i make a bad cut and pest if you tryed my line like that is
>> wrong less
>> coordinates input in -c
>>
>> $AMBERHOME/exe/sander.1cpu -O -i min1.in -o min1.out -p taxol.prmtop -c
>> taxol.inpcrd -r min1.rst -ref taxol.inpcrd
>>
>> the problem with refc error i'm sure could be solved add the ref
>> coordinate
>> try again and if you have the error mdfil about min1.rst try to look your
>> script
>> to run minstep1.
>>
>>
>> DAvide
>>
>>
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>>
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>>
>>
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>>
>>
GQ6RLsDn7Jtbt0bAwxrbXYB2PaAd19ZzWXergp4gOORSLV2/IrEHs+i5Uyr1MrqLo0BmoEMhqRsF9T98
>> gcJx2cXMB1+Ds=
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>>
>>
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>> :references;
>>
>>
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>>
>>
JODtPwBN1i7jIOZIpbVJVVn597tqL2xxwwEjsCnNIChb5eVNKooIyNCBnplKXKpQC16Oegt9k+3pMqp4
>> ggJcfGXr6xW14=
>> >Date: Mon, 16 Jul 2007 17:08:18 -0700
>> >From: "Lili Peng" <lilipeng.gmail.com>
>> >To: amber.scripps.edu
>> >Subject: Re: AMBER: refc error
>> >MIME-Version: 1.0
>> >X-Bayes-Prob: 0.0001 (Score 0)
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>>
>>
HTML_MESSAGE,J_CHICKENPOX_56,J_CHICKENPOX_57,PIPE_OBFUSCATION,SPF(pass,0),Mismat
>> ch(lilipeng.gmail.com mismatches mu-out-0910.google.com,2)
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>> >Davide,
>> >
>> >Thanks for your quick response. I tried that line but I got the error:
>> >
>> > mdfil: Error unknown flag: min1.rst
>> >
>> >
>> > usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
>> > [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip
>> -rdip
>> >rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo
>> >-radii radii]Consult the manual for additional options.
>> >
>> >other suggestions are welcome.
>> >
>> >Lili
>> >
>> >On 7/16/07, Davide Moiani <moiani.scripps.edu> wrote:
>> >>
>> >> Hi ,
>> >> when you use a restrain and you have ntr=1 sander request you -ref .crd
>> >>
>> >> $AMBERHOME/exe/sander.1cpu -O -i min1.in -o min1.out -p taxol.prmtop -c
>> >> -r min1.rst -ref taxol.inpcrd
>> >> Can you try that line if it works.
>> >>
>> >> Davide
>> >>
>> >>
>> >>
>> >> >DKIM-Signature: a=rsa-sha1; c=relaxed/relaxed; d=gmail.com; s=beta;
>> >>
>> >>
>>
>>
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>> >> sion:content-type;
>> >>
>> >>
>>
>>
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>> >>
>> >>
>>
>>
sK10mHffDy/uqsGO0x7J8+6STMDGhLJduQYWsUJZwTw3JCPcvNucYNznYMR8LcN3VMfccqaN3KU/wn0a
>> >> WfYVylLeP81J0=
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>> >>
>>
>>
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>> >>
>> >>
>>
>>
B80qGQyxrEEHBdO7fCD1wSTdQl6VEvEAZBZXIwWpt5BYPGTbNNNbuuMBy/9z1xHINCMJfVtlGjmjoN62
>> >> DBfuPmv99R+Xk=
>> >> >Date: Mon, 16 Jul 2007 16:56:11 -0700
>> >> >From: "Lili Peng" <lilipeng.gmail.com>
>> >> >To: amber.scripps.edu
>> >> >Subject: AMBER: refc error
>> >> >MIME-Version: 1.0
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>> >> >
>> >> >Dear all,
>> >> >
>> >> >I am having trouble running a restrained energy minimization on an
>> >> organic
>> >> >molecule. When I try to run it in Sander, I type in:
>> >> >
>> >> >" $AMBERHOME/exe/sander.1cpu -O -i min1.in -o min1.out -p taxol.prmtop-c
>> >> >taxol.inpcrd -r min1.rst "
>> >> >
>> >> >My min1.in consists of:
>> >> >
>> >> >" Initial minimization of structure
>> >> >&cntrl
>> >> > imin=1, maxcyc=200,
>> >> > ntpr=10,
>> >> > ntr=1,
>> >> > ibelly=1,
>> >> > bellymask=':1-20',
>> >> >/
>> >> >"
>> >> >However, when I try running the minimization, I get the error:
>> >> >" Unit 10 Error on OPEN: refc"
>> >> >
>> >> >I Googled this problem, and I get some hits about specifying a refc
>> file.
>> >> >How do I go about doing so?
>> >> >
>> >> >Thanks in advance,
>> >> >Lili
>> >>
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Received on Wed Jul 18 2007 - 06:07:51 PDT
