[Chimera-users] TER characters between residues in exported PDB ?

[Marek Maly]

Thanks !

I'll take a look on it.

   Best wishes,

       Marek



Dne Thu, 07 Jun 2012 22:07:16 +0200 Elaine Meng <meng at cgl.ucsf.edu>  
napsal/-a:

> I forgot to mention:  very recently we updated to AmberTools 12, so if  
> you want the latest recommended force field (ff12SB), please get a new  
> daily build.
>
> <http://www.cgl.ucsf.edu/chimera/download.html#daily>
>
> Elaine
>
> On Jun 7, 2012, at 12:12 PM, Elaine Meng wrote:
>
>> Hi Marek,
>> If you are going to use Amber, might as well just use Write Prmtop  
>> instead (in menu under Tools... Amber):
>> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html>
>>
>> This saves both a prmtop file and a inpcrd file.
>> Best,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>>
>> On Jun 7, 2012, at 11:19 AM, Marek Maly wrote:
>>
>>> Hello all,
>>>
>>> I would like to know if there is any way how to export from Chimera  
>>> molecular structure in  PDB format
>>> but with TER string between all residues in the file.
>>>
>>> This would be very helpful if one prepares in Chimera PDB inputs  
>>> (containing also non protein or non DNA/RNA molecules)
>>> for Amber because Amber (Leap) automatically tries to create bonds  
>>> between all consecutive residues unless they are separated
>>> by TER string.
>>>
>>> Thank you very much for any useful information.
>>>
>>>   Best wishes,
>>>
>>>      Marek
>>
>>
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>
>
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