Sure, leap does not know residue ADE, it only knows A for RNA (or DA for DNA). You can map ADE to A in your leaprc or you can rename the residues in your PDB ....Same for the other bases .... Did you go through the Amber tutorials before starting with your own stuff?
Vlad
On March 5, 2016 8:26:03 AM GMT+01:00, Sreemol G <sreemolinfo.gmail.com> wrote:
>I have PDB structure of RNA molecule. in that adenine, guanine,
>cytosine
>and uracil are named as ADE, GUA, CYT and URI respectively. while
>loading
>it in xleap i got the message "unknown residues:" and "created a new
>atom
>named: O2 within residues: ... etc".
>then i viewed my molecule in xleap i found it was completely distorted
>and
>all connections between the molecules were disconnected. and It looks
>totally different from the actual PDB structure.
>
>On Sat, Mar 5, 2016 at 12:44 PM, Jason Swails <jason.swails.gmail.com>
>wrote:
>
>> On Sat, Mar 5, 2016 at 2:04 AM, Sreemol G <sreemolinfo.gmail.com>
>wrote:
>>
>> > Hello all,
>> >
>> > Can anyone please tell me how adenine, thymine, cytosine, Guanine
>and
>> > uracil are defined in leap??
>> >
>>
>> The normal way?
>>
>> Do you have a more specific question? You can use the "edit" command
>in
>> xleap to investigate individual residues after you load a force
>field. For
>> example, inside xleap:
>>
>> source leaprc.ff14SB
>> edit A
>>
>> That will show you adenine
>>
>> edit DA
>>
>> That will show you deoxyadenine.
>>
>> (These residues are actually defined in the residue template
>libraries that
>> are loaded as part of a force field, not actually by leap itself).
>But I
>> can't expect to give information useful to you unless you provide a
>more
>> concrete description of what it is you are trying (but unable) to do.
>>
>> HTH,
>> Jason
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>--
>With kind regards,
>G. Sreemol
>M.Tech (Computational Biology)
>Anna university
>Chennai.
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>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
--
Sent from my Android device with K-9 Mail. Please excuse my brevity.
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Received on Sat Mar 05 2016 - 01:30:04 PST
