AMBER Archive (2007)

Subject: Re: AMBER: refc error

From: Lili Peng (lilipeng_at_gmail.com)
Date: Tue Jul 17 2007 - 17:40:26 CDT

Davide and Dr. Case,

That worked. Thanks for your help!

Lili

On 7/17/07, Davide Moiani <moiani_at_scripps.edu> wrote:
>
> 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
>
> >X-Authentication-Warning: trap.scripps.edu: defang set sender to
> lilipeng_at_gmail.com using -f
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>
> MfTqJVs4Gx/yxMRwF+DuJxGStZdgJxFoAyd6s8IFbRZeYAZ2Dch1zU39wp5xIKJKLK+Zt579bQqQfAP0
> asZHMndqgbZuw=
> >DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=beta;
>
> h=received:message-id:date:from:to:subject:in-reply-to:mime-version:content-type
> :references;
>
> b=APj7bfIbb6Z7mFh0g+lBcTNp9mCaGK1dbdFvRRYzpTF9KXXakM9CAa8Y9B2Tpf8ff8+F6ehleZ97H2
>
> RO5GvdKLBjfWxB6kK5fSJGaGjVNYiheE7lCwNN6qTojitvaHK0Cu2xpK/h6F3F/T5+mvQoMhuDGnBtI7
> wxtyMR3XFV3HU=
> >Date: Tue, 17 Jul 2007 11:35:06 -0700
> >From: "Lili Peng" <lilipeng_at_gmail.com>
> >To: amber_at_scripps.edu
> >Subject: Re: AMBER: refc error
> >MIME-Version: 1.0
> >X-Spam-Score: undef - spam scanning disabled
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> hermes
> >X-Virus-Status: Clean
> >
> >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_at_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
> >>
> >>
> >> >DKIM-Signature: a=rsa-sha1; c=relaxed/relaxed; d=gmail.com; s=beta;
> >>
> >>
>
> h=domainkey-signature:received:received:message-id:date:from:to:subject:in-reply
> >> -to:mime-version:content-type:references;
> >>
> >>
>
> b=OkstpsUTkAq9+u7RtGoSBls8qvBTUmFv7qNp+SycQ3sgVLAMKfakBlDx/D3vL/EJafegb9RpJtRNI4
> >>
> >>
>
> GQ6RLsDn7Jtbt0bAwxrbXYB2PaAd19ZzWXergp4gOORSLV2/IrEHs+i5Uyr1MrqLo0BmoEMhqRsF9T98
> >> gcJx2cXMB1+Ds=
> >> >DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=beta;
> >>
> >>
>
> h=received:message-id:date:from:to:subject:in-reply-to:mime-version:content-type
> >> :references;
> >>
> >>
>
> b=C96yTH8/gcy8142JGMPxxXKEQZUGjhSk6IOsT7rKZoBj+THUdk7fMJPbXAi+KsBXdhD5aSQ5C01h4U
> >>
> >>
>
> JODtPwBN1i7jIOZIpbVJVVn597tqL2xxwwEjsCnNIChb5eVNKooIyNCBnplKXKpQC16Oegt9k+3pMqp4
> >> ggJcfGXr6xW14=
> >> >Date: Mon, 16 Jul 2007 17:08:18 -0700
> >> >From: "Lili Peng" <lilipeng_at_gmail.com>
> >> >To: amber_at_scripps.edu
> >> >Subject: Re: AMBER: refc error
> >> >MIME-Version: 1.0
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> >>
> >>
>
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> >> ch(lilipeng_at_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_at_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;
> >> >>
> >> >>
> >>
> >>
>
> h=domainkey-signature:received:received:message-id:date:from:to:subject:mime-ver
> >> >> sion:content-type;
> >> >>
> >> >>
> >>
> >>
>
> b=GWmDFDsbnFX3/WBKt3H4LHwNWRYOGvWAyeuG5CkSIVMWd/Sn+IaGehS3qqMG7gVTGDXwqsluzHCWoJ
> >> >>
> >> >>
> >>
> >>
>
> sK10mHffDy/uqsGO0x7J8+6STMDGhLJduQYWsUJZwTw3JCPcvNucYNznYMR8LcN3VMfccqaN3KU/wn0a
> >> >> WfYVylLeP81J0=
> >> >> >DomainKey-Signature: a=rsa-sha1; c=nofws; d=gmail.com; s=beta;
> >> >>
> h=received:message-id:date:from:to:subject:mime-version:content-type;
> >> >>
> >> >>
> >>
> >>
>
> b=U+DVskrNhU+6K13QRx2da12CNZYqJAW1Vnms/QiY1Iur1fkReHlNNPF8C5CgurljfJosC/eRHangu8
> >> >>
> >> >>
> >>
> >>
>
> B80qGQyxrEEHBdO7fCD1wSTdQl6VEvEAZBZXIwWpt5BYPGTbNNNbuuMBy/9z1xHINCMJfVtlGjmjoN62
> >> >> DBfuPmv99R+Xk=
> >> >> >Date: Mon, 16 Jul 2007 16:56:11 -0700
> >> >> >From: "Lili Peng" <lilipeng_at_gmail.com>
> >> >> >To: amber_at_scripps.edu
> >> >> >Subject: AMBER: refc error
> >> >> >MIME-Version: 1.0
> >> >> >X-Bayes-Prob: 0.0001 (Score 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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