<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="country-region"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="City"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PersonName"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceName"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="PlaceType"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:595.45pt 841.7pt;
margin:1.0in 1.0in 1.0in 1.0in;}
div.Section1
{page:Section1;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang=EN-US link=blue vlink=blue>
<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>To eliminate O2*, check xlateat.dat under top
of share directory of Gromacs. It is a replacement table. To fix arbitrary PDB
file, checking the rtp file from FF usually helps.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Yang Ye<o:p></o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Tsjerk Wassenaar<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, February 02, 2006
2:59 PM<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">Discussion
list for GROMACS users</st1:PersonName><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [gmx-users]
converting pdb to gmx successfully - how?</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Hi David,<br>
<br>
Yeah, wouldn't we all want to be able to take arbitrary pdb files, run them
through a black box, fixing missing atoms, residues, deviations from naming
conventions, etc, etc. But, to cope with reality rather than ideality, you can
try to run the structure after (4) through pdb2gmx using the option -ignh. If
you then still have long bond warnings, this either means that your structure
misses stretches of residues or that seperate chains are being connected. The
latter you can deal with by assigning chain identifiers, though introducing TER
statements should also work. You can find more practical notes on using Gromacs
with DNA/RNA in the Gromacs user list archive. <br>
<br>
Good luck,<br>
<br>
Tsjerk<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><span class=gmailquote><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>On 2/1/06, <b><span style='font-weight:bold'>David
Mathog</span></b> <<a href="mailto:mathog@caltech.edu">mathog@caltech.edu</a>>
wrote:</span></font></span><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Short version:<br>
<br>
I want to be able to feed an arbitrary pdb file through<br>
some program such that pdb2gmx will accept the result.<br>
What is "some program"???<br>
<br>
Long version:<br>
<br>
I'm having trouble getting a structure with DNA and protein <br>
through pdb2gmx. Initially this began with warnings about "atom
O2* is<br>
missing". Attempts to fix that broke the protein
part. The PDB spec<br>
says that columns 18-20 are the residue name. The topology file <br>
says to use ADE for the RNA form and DADE for the DNA (etc.) DADE<br>
won't fit in 3 characters so presumably pdb2gmx accepts some other<br>
broader syntax for a "PDB" file.<br>
<br>
0. pdb2gmx doesn't know what C,G,T,A sre. <br>
<br>
1. Try the RNA forms (A->ADE etc) in cols 18-20, see if it<br>
autodetects DNA. Nope, O2* messages.<br>
<br>
2. Add a D in col 17. Result same as 1.<br>
<br>
3. Leave a space in column 17 and put DADE in 18-21. This <br>
A: breaks the PDB file format<br>
B: eliminated the O2* warnings<br>
C: left the H4 and H6 warnings (Xray structure, so of course<br>
no hydrogens)<br>
D: emitted a ton of "Warning: Long Bond" message for many, many <br>
pairs of atoms in the nucleic acid part of the file.<br>
<br>
4. Ran the pdb file through pdb2pqr web server. Then<br>
changed A->ADE,etc, ran that through pdb2gmx, and this time<br>
no warnings or errors (in the nucleic acid part). <br>
<br>
5. Took the pdb file from 4 and changed ADE->DADE (breaking PDB<br>
format). This worked the same as 4.<br>
<br>
Then I realized pdb2gmx was just blowing up in 4,5 because<br>
pdb2pqr was introducing an HA on the first <st1:place w:st="on">LYS</st1:place>,
so it wasn't <br>
even getting to the nucleic acid parts, which pdb2pqr moved to<br>
the end of the file (they were at the front before.)<br>
<br>
6. Found "protonate". Tried running the PDB file from (3)
through<br>
it with:<br>
<br>
protonate -s dpeptide1<br>
<br>
which blew up when 0 (system) was selected with:<br>
Fatal error:<br>
<br>
Atom -C not found in residue LYS39 while adding hydrogens<br>
<br>
-------------------------------------------------------- <br>
<br>
At which point I gave up and wrote this note.<br>
<br>
Thanks,<br>
<br>
David Mathog<br>
<a href="mailto:mathog@caltech.edu">mathog@caltech.edu</a><br>
Manager, Sequence Analysis Facility, Biology Division, Caltech<br>
_______________________________________________ <br>
gmx-users mailing list <a
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please don't post (un)subscribe requests to the list. Use the <br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php
</a><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br clear=all>
<br>
-- <br>
<br>
Tsjerk A. Wassenaar, M.Sc.<br>
<st1:City w:st="on"><st1:place w:st="on">Groningen</st1:place></st1:City>
Biomolecular Sciences and Biotechnology Institute (GBB)<br>
Dept. of Biophysical Chemistry<br>
<st1:place w:st="on"><st1:PlaceType w:st="on">University</st1:PlaceType> of <st1:PlaceName
w:st="on">Groningen</st1:PlaceName></st1:place><br>
Nijenborgh 4<br>
9747AG <st1:City w:st="on">Groningen</st1:City>, The <st1:country-region w:st="on"><st1:place
w:st="on">Netherlands</st1:place></st1:country-region><br>
+31 50 363 4336<o:p></o:p></span></font></p>
</div>
</body>
</html>