[gmx-users] Heme group with CHARMM27 FF

[Mark Abraham]

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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