Dear Abraham,
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.
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.
My problem is how to update .hdb with heme hydrogen details.
So, here to follow your suggestion removing the hydrogen atoms I wish to ignore
I actually need to ignore the hydorgens in protein.
Thanks
Sundar
-----Original Message-----
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Fri, Apr 20, 2012 8:08 pm
Subject: Re: [gmx-users] Heme group with CHARMM27 FF
On 20/04/2012 9:02 PM, Sundar Jubilant wrote:
Dear Abraham,
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.
You've never actually told us what hydrogens you want to ignore, so
you're making it hard to help you.
Mark
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.
Thanks for your information.
Sundar
-----Original Message-----
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users
<gmx-users@gromacs.org>
Sent: Fri, Apr 20, 2012 6:42 pm
Subject: Re: [gmx-users] Heme group with CHARMM27 FF
On 20/04/2012 7:33 PM, Sundar Jubilant wrote:
Dear Abraham,
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.
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.
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?
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.
Mark
Thanks
Sundar
-----Original Message-----
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users
<gmx-users@gromacs.org>
Sent: Fri, Apr 20, 2012 3:57 pm
Subject: Re: [gmx-users] Heme group with CHARMM27
FF
On 20/04/2012 4:38 PM, Sundar Jubilant wrote:
Dear Abraham,
Thanks for your email. I have already
read the manual to solve the problem
but I wasn't successful.
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.
I need little more detailed answer to
solve the problem.
By the way, here is the full command
line for which I got the error.
$ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb
-p CYP1_CHARMM.top -i CYP_CHARMM.itp
-ignh
If you don't ignore hydrogens, and they're
already correct, you don't need to re-generate
them...
Mark
The error is
WARNING:
atom HA is missing in residue HEM 513 in
the pdb file
You might need to add
atom HA to the hydrogen database
of building block HEME
in the file
aminoacids.hdb (see the manual)
WARNING: atom HB is missing in
residue HEM 513 in the pdb file
You might need to add
atom HB to the hydrogen database
of building block HEME
in the file
aminoacids.hdb (see the manual)
WARNING: atom HC is missing in
residue HEM 513 in the pdb file
You might need to add
atom HC to the hydrogen database
of building block HEME
in the file
aminoacids.hdb (see the manual)
.
.
.
.
.
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c,
line: 1449
Fatal error:
There were 30 missing atoms in
molecule Protein, if you want to
use this incomplete topology
anyhow, use the option -missing
For more information and tips
for troubleshooting, please
check the GROMACS
website at
http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Thanks.
Sundar Jubilant
-----Original Message-----
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users
<gmx-users@gromacs.org>
Sent: Fri, Apr 20, 2012 2:17 pm
Subject: Re: [gmx-users] Heme group with
CHARMM27 FF
On 20/04/2012 2:33 PM, Sundar Jubilant
wrote:
Dear gmx-users,
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 .
When asking for help, please give your
full command lines and/or interactive
selections so that we can know more
context.
WARNING: atom HA is missing in
residue HEM 513 in the pdb
file
You might need to add
atom HA to the hydrogen
database of building block
HEME
in the file
aminoacids.hdb (see the
manual)
WARNING: atom HB is missing in
residue HEM 513 in the pdb
file
You might need to add
atom HB to the hydrogen
database of building block
HEME
in the file
aminoacids.hdb (see the
manual)
WARNING: atom HC is missing in
residue HEM 513 in the pdb
file
You might need to add
atom HC to the hydrogen
database of building block
HEME
in the file
aminoacids.hdb (see the
manual)
.
.
.
.
.
-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: pdb2top.c,
line: 1449
Fatal error:
There were 30 missing atoms in
molecule Protein, if you want
to use this incomplete
topology anyhow, use the
option -missing
For more information and tips
for troubleshooting, please
check the GROMACS
website at
http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Can anyone help how can I
generate and add hydrogen
database information for heme
to be used with CHARMM27 ff?
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!)
Mark
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