Hi, all. I prepared the prmtop and inpcrd files of a complex, and I checked its validity with Parmed checkValidity and it says it looks good to it. Then I used cpptraj to check structure and it give following warning:
Warning: Atoms 223007:WAT_53527.H2 and 223008:WAT_53527.EPW are close (0.78)(This is for many water molecules, I just added one.)
Warning: Unusual bond length 9115:HIE_584.CE1 to 9117:HIE_584.NE2 (2.55)
Warning: Unusual bond length 9117:HIE_584.NE2 to 9119:HIE_584.CD2 (3.24)
When I run minimization, it sometimes failed or sometimes run for initial cycles and then says segmentation failure (core dumped) and sometimes says there are high energy regions in structure (something like that). I am using simple CPU system, not GPU. Could it be possible due to this factor or some other factor? Please guide me how to correct the warning printed by cpptraj if it needs to be.
Thanking you in advance for your help.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 14 2024 - 23:00:02 PST
