Hi again,
In my knowledge, yes you can. But you need to read the relevant
documentation in AmberTools manual. Because i was using xleap i can't
tell the command from memory...
best
peker
On Tue, Feb 15, 2011 at 7:40 PM, vani panguluri <vanipanguluri.gmail.com> wrote:
> how can we delete that hydrogen atoms ,can we able to do this by using
> amber........
>
>
> Regards,
> Vani
>
> On Tue, Feb 15, 2011 at 6:29 PM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Tue, Feb 15, 2011, vani panguluri wrote:
>> >
>> > while loading the pdbfile it was displaying the following messages
>> > Created a new atom named: HN within residue: .R<LEU 544>
>> > Created a new atom named: 1HB within residue: .R<ALA 545>
>> > Created a new atom named: 2HB within residue: .R<ALA 545>
>> > Created a new atom named: 3HB within residue: .R<ALA 545>
>>
>> It looks like your pdb file does not follow standard nomenclature, and may
>> have the atom names in unexpected columns. First, the amide hydrogen
>> should
>> be named "H", not "HN". The naming of the hydrogens attached to CB in SER
>> and ALA also are not being recognized.
>>
>> One common option is to remove all the hydrogen atoms from the pdb file,
>> and
>> let Amber re-add them with the proper names.
>>
>> ....dac
>>
>>
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Received on Tue Feb 15 2011 - 17:00:04 PST
