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.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at 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.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at 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.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at 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.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at 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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