[gmx-users] Heme group with CHARMM27 FF

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 23 04:58:20 CEST 2012 

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.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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>>>
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>>
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>
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