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On 23/04/2012 12:01 PM, Sundar Jubilant wrote:
<blockquote
cite="mid:8CEEF0C266A44E1-AD0-1B1F@webmail-d047.sysops.aol.com"
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>
Sorry for making it hard. Since I am so new to this I
guess I am not explaining it clearly for you to help me.<br>
<br>
First of all I dont want to ignore any hydrogens but as
pdb2gmx was complaining about my system and suggested me
to add -ignh I did so.<br>
</font></div>
</font></font></blockquote>
<br>
Since that step introduces other problems, maybe the suggestion
wasn't the best approach. Identifying the real problem may lead to a
better solution than trouble-shooting an issue that arose from a
suggested solution. There's a lesson here about describing the whole
problem when seeking help, rather than just the immediate aspect.
People who might help want all the information you can give them.<br>
<br>
<blockquote
cite="mid:8CEEF0C266A44E1-AD0-1B1F@webmail-d047.sysops.aol.com"
type="cite"><font color="black" face="arial" size="2"><font
color="black" face="arial" size="2">
<div><font face="Arial, Helvetica, sans-serif">
<br>
My problem is how to update .hdb with heme hydrogen
details.<br>
<br>
So, here to follow your suggestion removing the hydrogen
atoms I wish to ignore I actually need to ignore the
hydorgens in protein.<br>
</font></div>
</font></font></blockquote>
<br>
Maybe. Depends on the original problem. Chopping out just a subset
of hydrogens with a text editor, leaving heme alone, solves a class
of problems simply without needing to use the brute-force "-ign and
rebuild" approach.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:8CEEF0C266A44E1-AD0-1B1F@webmail-d047.sysops.aol.com"
type="cite"><font color="black" face="arial" size="2"><font
color="black" face="arial" size="2">
<div><font face="Arial, Helvetica, sans-serif">
<br>
Thanks<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 <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 8:08 pm<br>
Subject: Re: [gmx-users] Heme group with CHARMM27 FF<br>
<br>
<div id="AOLMsgPart_2_361177c0-3a9b-4dac-88f8-93d98bfd0285">
On 20/04/2012 9:02 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>
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>
</font></div>
</font></font></blockquote>
<br>
You've never actually told us what hydrogens you want to
ignore, so you're making it hard to help you.<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>
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 <a moz-do-not-send="true"
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
moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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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