Re: [gmx-users] Heme group with CHARMM27 FF

[Mark Abraham]

On 23/04/2012 12:01 PM, Sundar Jubilant wrote:

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.

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.


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.

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.

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 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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