Yes, the way described previously.
You can always use some other editor, like Avogadro or Chimera, which might have a little more “up to date” GUI if you do not want to utilise ‘bond’ in leap or edit the connect information. These will allow you to copy, paste and bond together copies of “the same” input pdb monomer. Any files produced might need to be edited to work properly with amber and you need parameters for any “new” bonds formed.
Best regards
// Gustaf
> On 11 Nov 2020, at 04:06, Pinky Mazumder <pmazumder67.gmail.com> wrote:
>
> Dear Dr. David,
>
> Thank you for your response.
>
> Actually, I want to build a polymer using a monomer. So, is this possible
> to use "bond" command between two (.pdb) files?
>
> Thank you again!
>
> Sincerely,
> Pinky
>
> On Thu, Aug 27, 2020 at 7:10 AM David A Case <david.case.rutgers.edu> wrote:
>
>> On Wed, Aug 26, 2020, Pinky Mazumder wrote:
>>>
>>> I am trying to build a cross-linking polymer of lignin...
>>
>>> Could you please share if there are any other commands of generating PDB
>>> files, please let me know.
>>>
>>> After that I need to load it in xleap to perform the simulation.
>>
>> Once you have a PDB file describing the coordinates of the system you want
>> to
>> simulate, there are two main ways of adding cross-links:
>>
>> 1. Put the information into CONECT records in the PDB file. LEaP will
>> apply
>> these (although it's always good to use ParmEd to check after you have the
>> prmtop file). Some graphics programs might do this for you, or you can
>> use a
>> text editor to add them by hand.
>>
>> 2. Add "bond" commands to your LEaP script, describing the new bonds you
>> want.
>>
>> (I don't think you can do both 1 and 2: do one or the other).
>>
>> ...hope this helps....dac
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> Pinky, Sharmi
> AL,US
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Received on Wed Nov 11 2020 - 00:00:03 PST
