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

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 7 13:07:16 PDT 2012

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.



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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