Dear Dr. Case,
Thank you for your guidance. I was able to generate the topology.
Regards
On Sat, Nov 7, 2020 at 1:02 AM Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:
> Thank you Dr. Case.
> I didnot realise that could be done. I will try and report back
> Thank you again
>
> On Sat, Nov 7, 2020 at 12:50 AM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Sat, Nov 07, 2020, Ayesha Fatima wrote:
>>
>> >Created a new atom named: HT1 within residue: .R<NSER 1>
>> >Created a new atom named: HT2 within residue: .R<NSER 1>
>> >Created a new atom named: HT3 within residue: .R<NSER 1>
>> >Created a new atom named: HN within residue: .R<THR 2>
>> >Created a new atom named: HN within residue: .R<ILE 3>
>>
>> Your pdb file has non-standard hydrogen names; (you don't say where this
>> file came from.)
>>
>> Simplest fix is to use that --nohyd option in pdb4amber to remove all
>> the hydrogens from your pdb file. Then leap will build them back in
>> with the correct names. ("Correct" here means complying with
>> IUPAC/wwPDB standards.)
>>
>> If you think the input hydrogen positions are iportant, you could also use
>> a text editor to change the atom names in the PDB file, but it is unlikely
>> that this is necessary.)
>>
>> ....dac
>>
>>
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>
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Received on Fri Nov 06 2020 - 10:30:02 PST
