[gmx-users] Writing pdb snapshot with charge from gro trajectory

[Peter Kroon]

IIRC the pdb format only allows 1 character (2 with sign) for the
charge, so you can only use integer charges. Which is pretty useless in
a MD context. So note that if you write a "pdb" with partial charges,
you're not writing pdb anymore, and I doubt anything other than
handcrafted programs will be able to read it.


Peter


On 08-11-17 16:30, Dawid das wrote:
> Hi,
>
> I thought so because of what you said about PDB file. Yes, I will be of
> course able to do it with Python.
>
> Best wishes,
> Dawid
>
> 2017-11-08 12:04 GMT+01:00 João Henriques <joao.m.a.henriques at gmail.com>:
>
>> Hi,
>>
>> The PDB format is strict by definition (
>> http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html
>> ).
>> Every single character (and column) within a line has a specific purpose
>> and charges are not included there. I doubt trjconv or other gromacs tools
>> will allow you to tamper with it in such way. You can however make a simple
>> script to (i) parse the topology, (ii) match it with the PDB file, and
>> (iii) add an extra column at the end of the PDB with the respective
>> charges. This should be relatively simple to do with your favorite
>> scripting language.
>>
>> Cheers,
>> J
>>
>> On Wed, Nov 8, 2017 at 11:12 AM, Dawid das <addiw7 at googlemail.com> wrote:
>>
>>> Dear Gromacs Users,
>>>
>>> I have a trajectory of my MD simulation in *.gro format. Is it possible
>> to
>>> write the pdb snapshot
>>> from the trajectory so that the pdb file contains the atomic charge from
>>> top file?
>>> The charge should be put at the end of my pdb file.
>>>
>>> Best wishes,
>>> Dawid Grabarek
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