[gmx-users] how to use atom2cg.awk
Justin A. Lemkul
jalemkul at vt.edu
Mon May 11 15:35:09 CEST 2009
Justin A. Lemkul wrote:
>
>
> xi zhao wrote:
>> But CG structure and native PDB structure is very different, please
>> see my attaches.
>>
>>
>
> Remove the chain identifier from the input structure. You'll note that
> the x-coordinate of each atom in the output is the residue number, so
> the chain identifier is throwing off the awk field count.
>
> -Justin
>
>>
>> 4
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>
>>
>> --- *09年5月11日，周一, Justin A. Lemkul /<jalemkul at vt.edu>/* 写道：
>>
>>
>> 发件人: Justin A. Lemkul <jalemkul at vt.edu>
>> 主题: Re: [gmx-users] how to use atom2cg.awk
>> 收件人: "Gromacs Users' List" <gmx-users at gromacs.org>
>> 日期: 2009年5月11日,周一,下午8:33
>>
>>
>>
>> xi zhao wrote:
>> > Dear sir:
>> > This is my modified script, please see it! I take CG
>> simulations according to
>> http://md.chem.rug.nl/marrink/coarsegrain.html.
>> > Thank you !
>> >
>>
>> Then your structure should be built appropriately.
>>
>> -Justin
>>
>> >
>> > 4
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
>>
>> >
>> > --- *09年5月11日，周一, Justin A. Lemkul /<jalemkul at vt.edu
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/*
>> 写道：
>> >
>> >
>> > 发件人: Justin A. Lemkul <jalemkul at vt.edu
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>> > 主题: Re: [gmx-users] how to use atom2cg.awk
>> > 收件人: "Gromacs Users' List" <gmx-users at gromacs.org
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>> > 日期: 2009年5月11日,周一,下午6:49
>> >
>> >
>> >
>> > xi zhao wrote:
>> > > Dear Sir:
>> > > In fact, I have modified the script as you said, but the CG
>> > strucrute produced is not different in secondary strucure
>> with
>> > native PDB structure: CG structure became a line strucrue!
>> Please
>> > help me! Or give me a good script!
>> >
>> > Visualization is not an appropriate method to use to
>> determine the
>> > validity of your procedure. The CG model will look a bit
>> strange
>> > when rendered as "lines" in most visualization software.
>> You did
>> > modify each line of the script, inserting $5 between every
>> $4 and
>> > $6, correct?
>> >
>> > -Justin
>> >
>> > > Thank you very much!
>> > > Best regards! >
>> > > 4
>> >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>
>> >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>
>>
>> > >
>> > > --- *09年5月11日，周一, Justin A. Lemkul /<jalemkul at vt.edu
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>> >
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/*
>> 写道：
>> > >
>> > >
>> > > 发件人: Justin A. Lemkul <jalemkul at vt.edu
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>> >
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>> > > 主题: Re: [gmx-users] how to use atom2cg.awk
>> > > 收件人: "Gromacs Users' List" <gmx-users at gromacs.org
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>> >
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>> > > 日期: 2009年5月11日,周一,上午8:22
>> > >
>> > >
>> > >
>> > > xi zhao wrote:
>> > > > Dear sir :
>> > > > how to motify the $5 in details?
>> > > > Thank you!
>> > > >
>> > >
>> > > Use a text editor (vi, emacs, gedit, etc), like you
>> would to
>> > create
>> > > any script.
>> > >
>> > > -Justin
>> > >
>> > > >
>> > > >
>> > > > 4
>> > >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>
>> >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
>>
>> > >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>
>> >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>>
>>
>> > > >
>> > > > --- *09年5月8日，周五, Justin A. Lemkul
>> /<jalemkul at vt.edu
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>> > >
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>/*
>> > 写道：
>> > > >
>> > > >
>> > > > 发件人: Justin A. Lemkul <jalemkul at vt.edu
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>> > <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>
>> > >
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalemkul@vt.edu>>
>> > > > 主题: Re: [gmx-users] how to use atom2cg.awk
>> > > > 收件人: "Discussion list for GROMACS users"
>> > > <gmx-users at gromacs.org
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>> >
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>> > >
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>>
>> > > > 日期: 2009年5月8日,周五,下午6:46
>> > > >
>> > > >
>> > > >
>> > > > xi zhao wrote:
>> > > > >
>> > > > >
>> > > > > Dear Sirs:
>> > > > > I wang to know simulate coarse-graied
>> system using
>> > > gromacs, but
>> > > > I don not know how to use atom2cg.awk to
>> convert CG model!
>> > > > > Thank you very much!
>> > > > >
>> > > >
>> > > > ./atom2cg_v2.1_tryout.awk my.pdb > out.pdb
>> > > >
>> > > > Note that the script available online needs
>> to be
>> > modified to
>> > > > include a $5 between the $4 and $6 on each
>> line, otherwise
>> > > you will
>> > > > get an incorrectly-formatted .pdb file.
>> > > >
>> > > > -Justin
>> > > >
>> > > > > 4
>> > > >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>
>> >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
>>
>> > >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>
>> >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>
>>
>> > > >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>
>> >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>
>>
>> > >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>
>>
>> >
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844
>>
>>
>> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>>>>>
>>
>> > > > >
>> > > > >
>> > > > >
>> > > >
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>> > > > -- ========================================
>> > > >
>> > > > Justin A. Lemkul
>> > > > Ph.D. Candidate
>> > > > ICTAS Doctoral Scholar
>> > > > Department of Biochemistry
>> > > > Virginia Tech
>> > > > Blacksburg, VA
>> > > > jalemkul[at]vt.edu | (540) 231-9080
>> > > >
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> > > >
>> > > > ========================================
>> > > > _______________________________________________
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>> > >
>> > >
>> > > -- ========================================
>> > >
>> > > Justin A. Lemkul
>> > > Ph.D. Candidate
>> > > ICTAS Doctoral Scholar
>> > > Department of Biochemistry
>> > > Virginia Tech
>> > > Blacksburg, VA
>> > > jalemkul[at]vt.edu | (540) 231-9080
>> > >
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> > >
>> > > ========================================
>> > > _______________________________________________
>> > > gmx-users mailing list gmx-users at gromacs.org
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>> >
>> >
>> > -- ========================================
>> >
>> > Justin A. Lemkul
>> > Ph.D. Candidate
>> > ICTAS Doctoral Scholar
>> > Department of Biochemistry
>> > Virginia Tech
>> > Blacksburg, VA
>> > jalemkul[at]vt.edu | (540) 231-9080
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> > ========================================
>> > _______________________________________________
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>> >
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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