AMBER Archive (2006)

Subject: AMBER: problems with Calcium ions treatment in GB run

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Thu Dec 28 2006 - 17:44:23 CST

Hi
I am trying to run mmpbsa calculations (or just single step GB min)
for the system containing 3 calcium ions. I prepared external ca.lib
for leap where I defined calcium ion using residue and atom name: C0 (Czero).
When I run calculations for without igb option on - everything seems to be ok.
Unfortunately, after turning igb into 1 or 2 I got warnings that my system
contains unusual nbond for C atoms:

Potential function:
     ntf = 1, ntb = 0, igb = 2, nsnb = 99999
     ipol = 0, gbsa = 1, iesp = 0
     dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
     saltcon = 0.00000, offset = 0.09000, gbalpha= 0.80000
     gbbeta = 0.00000, gbgamma = 2.90912, surften = 1.00000
     rdt = 0.00000, rgbmax = 25.00000
     alpb = 0
     scnb = 2.00000, scee = 1.20000
 
Frozen or restrained atoms:
     ibelly = 0, ntr = 0
 
Energy minimization:
     maxcyc = 1, ncyc = 0, ntmin = 1
     dx0 = 0.01000, drms = 0.00010
 Unusual nbond for C : 2459 0
  Using default carbon LCPO parameters
 Unusual nbond for C : 2460 0
  Using default carbon LCPO parameters
 Unusual nbond for C : 2461 0
  Using default carbon LCPO parameters
| INFO: Old style inpcrd file read
                                                                                                                 

Apparently my calcium ions "C0" that have atom numbers: 2459, 2460, 2461
are treated as "C" atoms in mdread.f of sander around line: 1200.

How to solve that problem?

Thanks
Piotr

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