[gmx-users] Heme group with CHARMM27 FF

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 20 13:07:42 CEST 2012 

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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