From: Shoresh Shafei (s.shafei_at_gmail.com)
Date: Sun Jan 25 2015 - 19:06:23 CST
When I perform minimization using namd for proteins solvated in water I notice that the water angles are drastically deviated from 104.5. Have you ever had this problem? How did you fix it? For more information, here are the steps I take:
1. I use amber to build the topology and crd files.
2. The water model is TIP3P
3. The generated pdb files by tLeap (Amber) are perfectly fine with regards to the water angles as well as the bond lengths; They all obey the TIP3P model.
4. After the minimization, the average angle of water molecules is around 99 degrees.
5. If I use SHAKE or SETLLE algorithms, the water bonds remain rigid however, the water angles still deviates drastically from 104.5.
6. As I read somewhere, one possibility is that the new versions of AMBER do not record the water angle in the topology file and consequently it is not read by namd. But a colleague of mine is performing DNA simulations using CHARMM (instead of amber) force field in namd and he has the same problem with water angles.
Please let me know if I need to provide any further information.
I appreciate your comments.
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