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 !
--- 09年5月11日，周一, Justin A. Lemkul <jalem...@vt.edu> 写道：
发件人: Justin A. Lemkul <jalem...@vt.edu>
主题: Re: [gmx-users] how to use atom2cg.awk
收件人: "Gromacs Users' List" <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>
>
> --- *09年5月11日，周一, Justin A. Lemkul /<jalem...@vt.edu>/* 写道：
>
>
> 发件人: Justin A. Lemkul <jalem...@vt.edu>
> 主题: Re: [gmx-users] how to use atom2cg.awk
> 收件人: "Gromacs Users' List" <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>>
> >
> > --- *09年5月8日，周五, Justin A. Lemkul /<jalem...@vt.edu
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/* 写道：
> >
> >
> > 发件人: Justin A. Lemkul <jalem...@vt.edu
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>
> > 主题: Re: [gmx-users] how to use atom2cg.awk
> > 收件人: "Discussion list for GROMACS users"
> <gmx-users@gromacs.org
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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>>>
> > >
> > >
> > >
> >
>------------------------------------------------------------------------
> > > 好玩贺卡等你发，邮箱贺卡全新上线！
> >
><http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
> >
> > >
> > >
> > >
> >
>------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > gmx-users mailing list gmx-users@gromacs.org
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
> >
><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search
> before
> > posting!
> > > Please don't post (un)subscribe requests to the list. Use
> the www
> > interface or send it to gmx-users-requ...@gromacs.org
>
><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>
> >
><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>.
> > > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> >
> > -- ========================================
> >
> > 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@gromacs.org
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
> >
><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org
>
><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>
> >
><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> >
> ------------------------------------------------------------------------
> > 好玩贺卡等你发，邮箱贺卡全新上线！
>
><http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/>
>
>
> -- ========================================
>
> 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@gromacs.org
> <http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org
>
><http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> ------------------------------------------------------------------------
> 好玩贺卡等你发，邮箱贺卡全新上线！
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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@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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___________________________________________________________
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http://card.mail.cn.yahoo.com/#!/usr/bin/awk -f
#Converts Atomic PDB file to Coarse-grain PDB file
#The atom types are default values - BN0, SC1, SC2
#Should be corrected by using correct itp file
#if columns are not separate (e.g. x or y or z > 99) the script doesnt work
#in that case insert an empty column or use PDBCat to separate columns
#d! groningen 29.01.08
{if
($1=="HEADER"||$1=="REMARK"||$1=="CRYST1"||$1=="MODEL"||$1=="TER"||$1=="ENDMDL"||$1=="END")
print $0
if($1=="ATOM" && $4=="ARG" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if($1=="ATOM" && $4=="ARG" && $3=="CG")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if($1=="ATOM" && $4=="ARG" && $3=="NE")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC2", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ALA" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ASN" && $3=="CA" )
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ASN" && $3=="CG")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ASP" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ASP" && $3=="CG")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="CYS" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="CYS" && $3=="SG")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="GLN" && $3=="CA" )
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="GLN" && $3=="CB")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="GLU" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="GLU" && $3=="CB")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="GLY" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="HIS" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="HIS" && $3=="CB")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="HIS" && $3=="ND1")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC2", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="HIS" && $3=="NE2")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC3", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ILE" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="ILE" && ($3=="CD" || $3=="CD1"))
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="LEU" && $3=="CA" )
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="LEU" && $3=="CG")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="LYS" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="LYS" && $3=="CG")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="LYS" && $3=="CE")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC2", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="MET" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="MET" && $3=="CG")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PHE" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PHE" && $3=="CG")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PHE" && $3=="CE1")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC2", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PHE" && $3=="CE2")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC3", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PRO" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="PRO" && $3=="CG")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="SER" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="SER" && $3=="CB")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="THR" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="THR" && $3=="CB")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TRP" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TRP" && $3=="CD1")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TRP" && $3=="CD2")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC2", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TRP" && $3=="CE2")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC3", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TRP" && $3=="CH2")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC4", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TYR" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TYR" && $3=="CG")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TYR" && $3=="CE1")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC2", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="TYR" && $3=="CE2")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC3", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="VAL" && $3=="CA")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"BN0", $4, $5, $6, $7, $8, $9,$10,$11);
else if ($1=="ATOM" && $4=="VAL" && $3=="CB")
printf("%4s %5i %4s %3s %4s %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2,
"SC1", $4, $5, $6, $7, $8, $9,$10,$11);
}
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