Dear all,
I've been running steered MD with AMBER 10 and I'm facing a kind of
weird problem. I use the same version of AMBER on 4 different
architectures. On 3 of them everything works fine, on the last one the
same input files yield very weird output in what is related to
restraints part. Here are these parts of the outputs:
1. Normal run:
R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 = 100.000 RK3 =
100.000
R1A= -45.000 R2A= 55.000 R3A= 55.000 R4A= 155.000 RK2A= 100.000 RK3A=
100.000
Rcurr: 14.989 Rcurr-(R2+R3)/2: 0.011 MIN(Rcurr-R2,Rcurr-R3): 0.011
-----------------------
2. "Weird output":
R1 = 115.000 R2 = 115.000 R3 = 115.000 R4 = 115.000 RK2 = 100.000 RK3 =
100.000
R1A= -45.000 R2A= 55.000 R3A= 55.000 R4A= 155.000 RK2A= 100.000 RK3A=
100.000
Rcurr: 14.989 Rcurr-(R2+R3)/2: 100.011 MIN(Rcurr-R2,Rcurr-R3): 100.011
-----------------------
Here is my restraints file, which is the same for both as well as input
file is the same:
------------------------
# Restraints for the centers of mass
&rst iat=-1,-1, r2=15.00, rk2=100, r2a=55.00, ir6=0, igr1=1095 ,
igr2=2115,2134,2144,2171,2177,2192,2213,2234,2241,2256,2270,2289,2301,2311,2330,2354,2366,2376,2395,2409,2416,
&end
---------------
In first case the given r2 in input is read correctly and r1, r3, r4 are
calculated automatically.
In the second case all r1, r2, r3 and r4 are wrongly assigned to the
value, which is equal to the r2 in input +100.
Did anyone face any similar problem?
Thank you very much in advance.
Best regards,
Sergey
--
Sergey A. Samsonov
Postdoctoral researcher
Structural Bioinformatics
Biotechnology Center
Tatzberg 47-51
01307 Dresden, Germany
Tel: (+49) 351 463 400 83
Fax: (+49) 351 463 402 87
E-mail: sergey.samsonov.biotec.tu-dresden.de
Webpage: www.biotec.tu-dresden.de
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 25 2011 - 05:00:02 PDT
