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On 20/04/2012 9:02 PM, Sundar Jubilant wrote:
<blockquote
cite="mid:8CEECFC44F2F8A7-410-3CDFE@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>
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
cite="mid:8CEECFC44F2F8A7-410-3CDFE@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>
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 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 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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