AMBER Archive (2007)

Subject: AMBER: amber9 possible failure tgtmd

From: jlalonde (jlalonde_at_brynmawr.edu)
Date: Fri Feb 09 2007 - 10:19:19 CST

Dear Users,

I have just installed Amber9 on a single node of a Beowulf cluster. The
serial test reported a possible failure in the targeted MD module (see
below). Has any one seen this error?

Thank you,
Judith

System intel xeon cpu 1500 mhz
i686
gfortran gcc 4.0.1
Red heat 4.0.105
Kernel 2.6.12-1.1456_FC4smp

./configure –p4 gfortran

Possible failures in tgtmd.out.diff in
/usr/local/amber9/test/tgtmd/change_target

< Mask ":3-10_at_CA,N,C,O,H,HA" matches 47 atoms 

---

 > Mask ":3-10_at_CA,N,C,O,H,HA" matches 58 atoms

Original 
trgmd.out.save----------------------------------------------------------------------

Targeted molecular dynamics:

tgtrmsd = 2.00000, tgtmdfrc= 1.00000

LOADING THE TARGETED MD ATOMS AS GROUPS

5. REFERENCE ATOM COORDINATES

Mask ":3-10_at_CA,N,C,O,H,HA" matches 47 atoms

Mask ":3-10_at_CA,N,C,O,H,HA" matches 47 atoms

New Test 
trgmd.out.----------------------------------------------------------------------

Targeted molecular dynamics:

tgtrmsd = 2.00000, tgtmdfrc= 1.00000

LOADING THE TARGETED MD ATOMS AS GROUPS

5. REFERENCE ATOM COORDINATES

| INFO: Old style inpcrd file read

Mask ":3-10_at_CA,N,C,O,H,HA" matches 58 atoms

Mask ":3-10_at_CA,N,C,O,H,HA" matches 47 atoms

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