<font color='black' size='2' face='arial'><font color="black" face="arial" size="2">
<div> <br>
</div>
<div> <font face="Arial, Helvetica, sans-serif">Dear Abraham,<br>
<br>
How would it work if I remove the hydrogen atoms that I wish to ignore from my input co-ordinate file? The pdb2gmx tries to add the missing hydorgen atoms for which the .hdb doesn't have information.<br>
<br>
In my case here, I can consider heme as a ligand instead of having it as protein since it doesn't need to be the part of the protein.<br>
<br>
Thanks for your information.<br>
Sundar<br>
</font>
</div>
<div> <br>
</div>
<div style="font-family:arial,helvetica;font-size:10pt;color:black">-----Original Message-----<br>
From: Mark Abraham <Mark.Abraham@anu.edu.au><br>
To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>
Sent: Fri, Apr 20, 2012 6:42 pm<br>
Subject: Re: [gmx-users] Heme group with CHARMM27 FF<br>
<br>
<div id="AOLMsgPart_2_3edbbaac-164b-4d4b-bb0b-675bb06150c4">
On 20/04/2012 7:33 PM, Sundar Jubilant wrote:
<blockquote type="cite"><font color="black" face="arial" size="2"><font color="black" face="arial" size="2">
<div> Dear Abraham,<br>
<br>
I am ignoring hydrogens for the protein residues since I am
not sure if the Gromacs has an option to ignore hydrogen
only for pretein residues but not for the heme complexed
with it.<br>
</div>
</font></font></blockquote>
<br>
No, there is no ability to ignore them selectively - but if you want
to ignore any of them, you have to address the heme hydrogen
database issue, or go and remove the hydrogen atoms that you wish to
ignore from your input coordinate file.<br>
<br>
<blockquote type="cite"><font color="black" face="arial" size="2"><font color="black" face="arial" size="2">
<div>
<br>
One of my colleagues suggested to treat the Heme as an
ligand not as a part of the protein to solve this issue. How
would that really affect the accuracy of the simulation?<br>
</div>
</font></font></blockquote>
<br>
It's not a question of accuracy, but rather that if you have bonded
interactions between heme and protein, they have to be part of the
same [moleculetype], which is what pdb2gmx is struggling to
generate.<br>
<br>
Mark<br>
<br>
<blockquote type="cite"><font color="black" face="arial" size="2"><font color="black" face="arial" size="2">
<div>
<br>
Thanks<br>
Sundar<br>
</div>
<div> <br>
</div>
<div> <br>
</div>
<div style="font-family:arial,helvetica;font-size:10pt;color:black">-----Original
Message-----<br>
From: Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
To: Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
Sent: Fri, Apr 20, 2012 3:57 pm<br>
Subject: Re: [gmx-users] Heme group with CHARMM27 FF<br>
<br>
<div id="AOLMsgPart_2_f2d1812f-0eae-4513-a2a5-23a35a3ae4bd">
On 20/04/2012 4:38 PM, Sundar Jubilant wrote:
<blockquote type="cite"><font color="black" face="arial" size="2"><font color="black" face="arial" size="2">
<div> <br>
</div>
<div> <font face="Arial, Helvetica, sans-serif">Dear
Abraham,<br>
<br>
Thanks for your email. I have already read the
manual to solve the problem but I wasn't
successful.<br>
</font></div>
</font></font></blockquote>
<br>
That's good to say (particularly the first time you post a
request for help, else you'll just get told to go and
read), but is unlikely to get much help because you
haven't identified a specific problem. You'd like the
ability to build hydrogen atoms on a heme residue. pdb2gmx
has to have a specific recipe for doing that. The manual
describes the required format and gives an example.
Someone's going to have to do some work.<br>
<br>
<blockquote type="cite"><font color="black" face="arial" size="2"><font color="black" face="arial" size="2">
<div><font face="Arial, Helvetica, sans-serif"> <br>
I need little more detailed answer to solve the
problem. <br>
<br>
By the way, here is the full command line for
which I got the error.<br>
<br>
$ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p
CYP1_CHARMM.top -i CYP_CHARMM.itp -ignh<br>
</font></div>
</font></font></blockquote>
<br>
If you don't ignore hydrogens, and they're already
correct, you don't need to re-generate them...<br>
<br>
Mark<br>
<br>
<blockquote type="cite"><font color="black" face="arial" size="2"><font color="black" face="arial" size="2">
<div><font face="Arial, Helvetica, sans-serif"> <br>
The error is<br>
<br>
</font><font color="black" face="arial" size="2"><font color="black" face="arial" size="2"><font color="black" face="arial" size="2"><font face="Arial, Helvetica, sans-serif">WARNING:
atom HA is missing in residue HEM 513 in
the pdb file<br>
You might need to add atom HA to
the hydrogen database of building block
HEME<br>
in the file aminoacids.hdb (see
the manual)<br>
<br>
<br>
WARNING: atom HB is missing in residue HEM
513 in the pdb file<br>
You might need to add atom HB to
the hydrogen database of building block
HEME<br>
in the file aminoacids.hdb (see
the manual)<br>
<br>
<br>
WARNING: atom HC is missing in residue HEM
513 in the pdb file<br>
You might need to add atom HC to
the hydrogen database of building block
HEME<br>
in the file aminoacids.hdb (see
the manual)<br>
<br>
.<br>
.<br>
.<br>
.<br>
.<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.5.3<br>
Source code file: pdb2top.c, line: 1449<br>
<br>
Fatal error:<br>
There were 30 missing atoms in molecule
Protein, if you want to use this
incomplete topology anyhow, use the option
-missing<br>
For more information and tips for
troubleshooting, please check the GROMACS<br>
website at <a class="moz-txt-link-freetext" target="_blank" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
Thanks.<br>
<br>
Sundar Jubilant<br>
</font></font></font></font><font face="Arial, Helvetica, sans-serif"><br>
</font> </div>
<div> <br>
</div>
<div style="font-family:arial,helvetica;font-size:10pt;color:black">-----Original
Message-----<br>
From: Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
Sent: Fri, Apr 20, 2012 2:17 pm<br>
Subject: Re: [gmx-users] Heme group with CHARMM27
FF<br>
<br>
<div id="AOLMsgPart_2_989141e2-b2c9-4465-ab1e-9f4619eb8577">
On 20/04/2012 2:33 PM, Sundar Jubilant wrote:
<blockquote type="cite"><font color="black" face="arial" size="2"><font color="black" face="arial" size="2"><font face="Arial, Helvetica, sans-serif">Dear gmx-users,<br>
<br>
I am new to Gromacs and trying to
simulate a protein with a heme group
using CHARMM27 ff in Gromacs 4.5.3. I
have received the following error while
running pdb2gmx .<br>
</font></font></font></blockquote>
<br>
When asking for help, please give your full
command lines and/or interactive selections so
that we can know more context.<br>
<br>
<blockquote type="cite"><font color="black" face="arial" size="2"><font color="black" face="arial" size="2"><font face="Arial, Helvetica, sans-serif"> <br>
WARNING: atom HA is missing in residue
HEM 513 in the pdb file<br>
You might need to add atom HA
to the hydrogen database of building
block HEME<br>
in the file aminoacids.hdb (see
the manual)<br>
<br>
<br>
WARNING: atom HB is missing in residue
HEM 513 in the pdb file<br>
You might need to add atom HB
to the hydrogen database of building
block HEME<br>
in the file aminoacids.hdb (see
the manual)<br>
<br>
<br>
WARNING: atom HC is missing in residue
HEM 513 in the pdb file<br>
You might need to add atom HC
to the hydrogen database of building
block HEME<br>
in the file aminoacids.hdb (see
the manual)<br>
<br>
.<br>
.<br>
.<br>
.<br>
.<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.5.3<br>
Source code file: pdb2top.c, line: 1449<br>
<br>
Fatal error:<br>
There were 30 missing atoms in molecule
Protein, if you want to use this
incomplete topology anyhow, use the
option -missing<br>
For more information and tips for
troubleshooting, please check the
GROMACS<br>
website at <a class="moz-txt-link-freetext" target="_blank" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
Can anyone help how can I generate and
add hydrogen database information for
heme to be used with CHARMM27 ff?</font></font></font><br>
</blockquote>
<font color="black"><font size="2"><font face="Arial, Helvetica, sans-serif"><br>
You'll have to read the applicable
sections of manual chapter 5, make a local
copy of the charmm27.ff folder in your
working directory and editing
aminoacids.hdb to add the generation
information. When you're done, please post
your efforts so that others might be able
to benefit from them in future. (Also,
search first in case this has already
happened!)<br>
<br>
Mark<br>
</font></font></font> </div>
<div id="AOLMsgPart_3_989141e2-b2c9-4465-ab1e-9f4619eb8577" style="margin: 0px;font-family: Tahoma, Verdana, Arial, Sans-Serif;font-size: 12px;color: #000;background-color: #fff;">
<pre style="font-size: 9pt;"><tt>--
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
Please search the archive at <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
Can't post? Read <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a>
</tt></pre>
</div>
</div>
</font></font> <br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</div>
<div id="AOLMsgPart_3_f2d1812f-0eae-4513-a2a5-23a35a3ae4bd" style="margin: 0px;font-family: Tahoma, Verdana, Arial, Sans-Serif;font-size: 12px;color: #000;background-color: #fff;">
<pre style="font-size: 9pt;"><tt>--
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
Please search the archive at <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
Can't post? Read <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a>
</tt></pre>
</div>
</div>
</font></font>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</div>
<!-- end of AOLMsgPart_2_3edbbaac-164b-4d4b-bb0b-675bb06150c4 -->
<div id="AOLMsgPart_3_3edbbaac-164b-4d4b-bb0b-675bb06150c4" style="margin: 0px;font-family: Tahoma, Verdana, Arial, Sans-Serif;font-size: 12px;color: #000;background-color: #fff;">
<pre style="font-size: 9pt;"><tt>--
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a>
</tt></pre>
</div>
<!-- end of AOLMsgPart_3_3edbbaac-164b-4d4b-bb0b-675bb06150c4 -->
</div>
</font></font>