pdb4amber command can do the purpose?
Cannot do manualy each time?
Need to embed in code.
On Thu 6 Feb, 2020, 12:30 AM ankita mehta, <mehtaroadies.gmail.com> wrote:
> Is it for
> 1. N terminal alanine residue or
> 2.Any N terminal residue
> 2. Rest of Alanines in file(IF they were present) or
> 3.all the other amino acids
>
>
> shouldn't have Hydrogen in it?
>
> On Thu 6 Feb, 2020, 12:16 AM David A Case, <david.case.rutgers.edu> wrote:
>
>> On Wed, Feb 05, 2020, ankita mehta wrote:
>>
>> >i wanted to generate prmtop and inpcrd files of attached pdb.
>> >But , it is giving me errors.
>>
>> If you haven't yet done so, do a Google search on Amber "does not have a
>> type". You'll get the general idea.
>>
>> Your pdb file has a N-terminal alanine with an H atom in it. But the
>> Amber library for alanine in an Nterminal position uses H1/H2/H3, but no
>> H.
>>
>> Simplest solution is to remove the H atom from the pdb file: tleap will
>> build in the H1/H2/H3 for you.
>>
>> ....dac
>>
>>
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>>
>
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Received on Wed Feb 05 2020 - 11:30:02 PST
