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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>Date: Mon, 16 Jul 2007 17:08:18 -0700
>From: "Lili Peng" <lilipeng.gmail.com>
>To: amber.scripps.edu
>Subject: Re: AMBER: refc error
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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
>>
>>
>>
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>>
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>>
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>>
>>
sK10mHffDy/uqsGO0x7J8+6STMDGhLJduQYWsUJZwTw3JCPcvNucYNznYMR8LcN3VMfccqaN3KU/wn0a
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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
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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 - 06:07:35 PDT
