<font color='black' size='2' face='arial'><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>
<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>
<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 <Mark.Abraham@anu.edu.au><br>
To: Discussion list for GROMACS users <gmx-users@gromacs.org><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>
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