[gmx-developers] modify pdb2gmx and/or g_protonate in order to add specific hydrogen name

[Landry Charlier]

Hi,

yes, by modifying this line, I can add letter instead of number.  
Nevertheless, the problem remains the same. I have to create a 'clone'  
of each lipid in the rtp file because the letter of hydrogen name  
begins by R or X following the fatty acid chains and begins by A for  
the polar head!
As you say Berk, "A proper solution would be to allow setting this  
starting character in the hdb file".
Or by directly putting the different names in the hdb like that '3 4  
H13A,H13B,H13C C13 N C12'.
But the two solutions implicate a modification of the code and I am  
not enough good for that.




Quoting Berk Hess <hess at kth.se>:

> Hi,
>
> I guess a single character change in the code should do it.
> Try changing line 279 of src/kernel/genhydro.c (in version 4.6) from
>                     (*abi)[*nabi + k].nname[l]   = '1' + k;
> to
>                     (*abi)[*nabi + k].nname[l]   = 'A' + k;
>
> A proper solution would be to allow setting this starting character  
> in the hdb file.
>
> Cheers,
>
> Berk
>
> On 02/04/2013 10:00 AM, Landry Charlier wrote:
>> Thank you for yours answers.
>>
>> I have already tried the solution of Dr. Abraham. Indeed for POPC I have:
>> - created a "clone" for POPC. Indeed, if i put the line "3 4 H13  
>> C13 N C12" in the lipid.hdb file, pdb2gmx will bug by saying that  
>> the atom H131 is not in the residue POPC.
>> So i have created the residue POPD, a clone of POPC in the  
>> lipid.rtp but with changes for the hydrogen names.
>> - filled the lipid.hdb for the residue POPD
>> - done a script with the sed command the change the residue name  
>> (POPD to POPC) and the hydrogen names.
>>
>> The problem is that I don't only work on POPC, I work on all the  
>> lipids contains in the charmm36. So I have to create a clone and a  
>> script for each lipid. Before doing all these steps, I have written  
>> this mail in order to know if there is an other solution.
>>
>> I think that the better (but may be not the easier) solution is to  
>> change the code. I will try the trick of Emanuel and if it's not  
>> good, I will do all the clones and scripts.
>>
>> Landraille
>>
>>
>>
>>
>>
>>
>>
>> Mark Abraham <mark.j.abraham at gmail.com> a écrit :
>>
>>> On Fri, Feb 1, 2013 at 7:40 PM, Emanuel Peter <
>>> Emanuel.Peter at chemie.uni-regensburg.de> wrote:
>>>
>>>> I would try in the hdb entry
>>>>
>>>> H12A C13 N C12
>>>> H13B C13 N C14
>>>> H13C C13 N C15
>>>>
>>>> or
>>>>
>>>> H12A C13 C12 C14
>>>> H13B C13 C12 C15
>>>> H13C C13 N C16
>>>>
>>>> and then afterwards minimize.....
>>>>
>>>> Others might know a better way.
>>>> This way was (for me) the easiest way.
>>>> After minimization I got a reasonable protonation.
>>>>
>>>
>>> Even if you can abuse pdb2gmx to put three hydrogens in like this, you
>>> still have to get lucky that EM can sort out the problems. If it's only a
>>> naming problem, it's much more reliable to rename the atoms...
>>>
>>> Best and good luck,
>>>>
>>>> Emanuel
>>>>
>>>>>>> Landry Charlier <landry.charlier at univ-montp1.fr> 02/01/13 12:51 AM >>>
>>>>
>>>>
>>>> Hello,
>>>>
>>>> I have some problems in order to automatically add hydrogen to lipids
>>>> with charmm36 force field. Indeed, when several hydrogen have to be
>>>> added to the same atom, the command pdb2gmx -ignh or g_protonate add
>>>> them with the same name but with the last number incremented by 1
>>>> thanks to the .hdb file.
>>>>
>>>> Example : for charmm36, the hydrogens added to the CB atom of ARG are
>>>> named HB1 & HB2 thanks to the line "2 6 HB CB CG CA" in the
>>>> aminoacids.hdb file.
>>>>
>>>> For lipids, the hydrogen names differ by a letter. H13A, H13B H13C are
>>>> linked to C13 in POPC in charmm36 for example.
>>>>
>>>> I would like to modify g_protonate or pdb2gmx in order to add hydrogen
>>>> with a specific name like that:
>>>> - If only 1 name is written in hdb file and several atoms have to be
>>>> added, the hydrogen names have been incremented by 1 as it's by
>>>> default (see the example of Arg above).
>>>> - If there are as many names as the number of hydrogen to add, pdb2gmx
>>>> and/or g_protonate will choose these names. The hdb file should be
>>>> like this : 3 4 H13A,H13B,H13C C13 N C12
>>>>
>>>> But I check the g_protonate and pdb2gmx files in the source code and I
>>>> am not enough good in programming for modify them.
>>>>
>>>> Could you help me please?
>>>>
>>>
>>> You've not been completely clear on why you need the atoms named
>>> differently, so I'll assume you need some output file from pdb2gmx to have
>>> atom names that match something else. If so, it is much easier to use sed
>>> three times to do the necessary changes than to think about touching C
>>> code. For example:
>>> sed -e 's/H131/H13A' infile > outfile
>>>
>>> Since you've got a script calling pdb2gmx anyway (hint, hint), you don't
>>> even have to remember the magic words once you write them!
>>>
>>> Mark
>>>
>>
>>
>>
>>
>
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