I have discovered two other potential errors in the script:
1. Coordinates are not processed quite right; this leads to a molecule with the
correct shape, but some residues are scrambled.
2. ILE residues are not handled correctly (only a backbone particle is
generated)
I modified the script, and it is working in my own internal tests. I would
suggest using the script below.
-Justin
-------
#!/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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %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 %4i %8.3f%8.3f%8.3f%6.2f%6.2f \n",$1, $2, "SC1",
$4, $5, $6, $7, $8, $9,$10,$11);
}
xi zhao wrote:
Dear Sir:
The script can produce correct structure,thank you very much!
Best regards!
Zhao xi
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,下午9:35
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
<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
<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: "Gromacs Users' List" <gmx-users@gromacs.org
<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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>
>>
<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
/<jalem...@vt.edu
<http://cn.mc151.mail.yahoo.com/mc/compose?to=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>
>> <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: "Gromacs Users' 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>>
>> > 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>>
>> >
<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
/<jalem...@vt.edu
<http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=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>
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=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: "Gromacs Users' 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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@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>>>
>> > >
<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
>> /<jalem...@vt.edu
<http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>
>> >
<http://cn.mc151.mail.yahoo.com/mc/compose?to=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>
>> <http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>
>> >
<http://cn.mc151.mail.yahoo.com/mc/compose?to=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>
>>
<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://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>>
>> >
<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>>
>> >
<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>>>>>>
>> > > > >
>> > > > >
>> > > > >
>> > > >
------------------------------------------------------------------------
>> > > > > 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>
>>
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>> >
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>> > >
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>> > > >
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>> > > > >
>> 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>
>> >
<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>
>> > > >
<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
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>>
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>> >
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>> > >
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>> > > >
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>> > > >
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>> > > > Please search the archive at
>> > http://www.gromacs.org/search before
>> > > > posting!
>> > > > Please don't post (un)subscribe
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>> > Use the
>> > > > www interface or send it to
>> > gmx-users-requ...@gromacs.org
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>>
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>> >
<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>
>> > > >
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>> > > > Can't post? Read
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>> > > >
>> > > >
>> > > >
>> > >
------------------------------------------------------------------------
>> > > > 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
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<http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
>>
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>> >
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>> > >
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>> > > 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>
>>
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>> >
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>> > >
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>> > > Can't post? Read
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>> > >
>> > >
>> > >
>> >
------------------------------------------------------------------------
>> > > 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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>
>>
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>> >
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>> > 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
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>>
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>> >
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>> > Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
>> >
>> >
>> >
>>
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>> > 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>
>>
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>> 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>
>>
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>> 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
========================================
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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
========================================
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