[gmx-users] [PyMOL] how to connect to atoms?

[Tsjerk Wassenaar]

Hi Leila,

This too is more a question for the Gromacs mailing list.
Gromacs does not read bond information (CONECT records) from a PDB file. It
only reads the ATOM/HETATM records and sets bonds based on the force field
building block definitions and the special bonds (such as the isopeptide
link) in the specbond.dat file.

Cheers,

Tsjerk

On Mon, May 11, 2015 at 10:02 PM, leila karami <karami.leila1 at gmail.com>
wrote:

> You are right. I will ask my question gromacs mailing list.
>
> But, please answer my first question.
>
> I create a covalent bond between these 2 atoms using hyperchem. After I
> saved new pdb file, the format of pdb file was changed. Which software or
> model builder is appropriate for this goal?
>
> Thanks in advance.
>
>
>
> ---------------------------------------------------
>
>
>
>
>
>
> *Dr. Leila KaramiPostdoctoral ResearcherInstitute of Biochemistry and
> BiophysicsUniversity of TehranTehran, Iran*
>
> *Email: karami.leila at ut.ac.ir <karami.leila at ut.ac.ir>
> <karami.leila at ut.ac.ir>*
> *Tel: +98 9193155894 <%2B98%209193155894>*
>
> On Tue, May 12, 2015 at 12:27 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
>> Hi Leila,
>>
>> Please ask this question on the gromacs mailing list. But first search
>> the gromacs archives to see what's already there (which is most of what you
>> ask).
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Mon, May 11, 2015 at 9:54 PM, leila karami <karami.leila1 at gmail.com>
>> wrote:
>>
>>> Dear Tsjerk
>>>
>>> Thanks for your quick answer.
>>>
>>> Yes, the peptides are already positioned correctly.
>>>
>>> Which option in pdb2gmx does make this bond between two residues from
>>> two different chains? I want to make covalent bond between two atoms (CD
>>> atom of GLU residue from peptide 1 and NZ atom of LYS residue from peptide
>>> 2). What you mentioned is related to merging of two chains.
>>>
>>> I am beginner in this field.
>>> Please guide about that.
>>>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>


-- 
Tsjerk A. Wassenaar, Ph.D.