1. I don't know whether AMBER could use four letters for the residue name. I thought it only allows three letters residue name

2. Did you use sequence and impose command to define the dihedrals?

3. I do not pay much attention to the initial structure. After a minimization, the structure would make sense.

4. Maybe you can define two kind VALA residues with opposite head and end to build a anti-parallel structure.

Hi Xiaoquan,

thank you so much for your response.

1. I have used only three letter code (ZLA) just to differentiate my question I have I indicated my block as VALA.

2. I have used

VK = sequence {ZLA ZLA ZLA ZLA ZLA ZLA ZLA ZLA}

impose VK  {1 2 3 4 5 6 7 8} {N CA CT N2 180} and

 impose VK  {1 2 3 4 5 6 7 8} {CA CT N2 CA 180}

 but it actually folded the structure in a circular manner.

3. Before carrying minimization I wanted know things are clear as regular amino acids.

4. This is a good suggestion, I will try to build new lib with opposite head.

Again, thank you so much for you suggestion and your time.

Best regards

Vasantha

Hi Xiaoquan

Finally, impose command worked. With my save ZLA.lib I could put each block in anti parallel.

Thank you-- Vasantha