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
>
>
> >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.gmail.com>
> >To: amber.scripps.edu
> >Subject: Re: AMBER: refc error
> >MIME-Version: 1.0
> >X-Bayes-Prob: 0.0001 (Score 0)
> >X-Spam-Score: 4.20 (****) [Hold at 5.00]
>
> 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)
> >X-CanItPRO-Stream: majordomo (inherits from default)
> >X-Canit-Stats-ID: 30734387 - 035cc1a19bca
> >X-Antispam-Training: Train as spam:
> >X-Antispam-Training: Train as non-spam:
> >X-Antispam-Training: Cancel training:
> >X-Scanned-By: CanIt (www . roaringpenguin . com) on 137.131.200.29
> >
> >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;
> >>
> >>
>
> 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.gmail.com>
> >> >To: amber.scripps.edu
> >> >Subject: AMBER: refc error
> >> >MIME-Version: 1.0
> >> >X-Bayes-Prob: 0.0001 (Score 0)
> >> >X-Spam-Score: 2.60 (**) [Hold at 5.00]
> >>
> HTML_MESSAGE,J_CHICKENPOX_56,SPF(pass,0),Mismatch(
> lilipeng.gmail.commismatches
> >> nf-out-0910.google.com,2)
> >> >X-CanItPRO-Stream: majordomo (inherits from default)
> >> >X-Canit-Stats-ID: 30733783 - 8c007af0fc7a
> >> >X-Antispam-Training: Train as spam:
> >> >X-Antispam-Training: Train as non-spam:
> >> >X-Antispam-Training: Cancel training:
> >> >X-Scanned-By: CanIt (www . roaringpenguin . com) on 137.131.200.30
> >> >
> >> >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
> >>
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber.scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jul 18 2007 - 06:07:50 PDT
