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