<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>
Thanks for your email. I have already read the manual to solve the problem but I wasn't successful.<br>
<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>
<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>
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<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 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>
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