Hi Amber community,
Greetings. I am running equilibration of one quaternary system composed of protein, DNA, Ligand and two Mg+2 ions. After minimization, as suggested by Amber developers, I carried out equilibration with langevian thermostat, without heating up the system, with harmonic constraints of 50.0 for solute.
In next step I removed the harmonic constraints and subjected it for equilibration. But I am getting this error as follows. I have attached the input files along with.
Could anyone please tell me, how can I solve the solution.
Regards
Pankaj
**************************************************************************************
p31_2777: p4_error: net_recv read: probable EOF on socket: 1
p30_2775: p4_error: net_recv read: probable EOF on socket: 1
p29_2773: p4_error: net_recv read: probable EOF on socket: 1
bm_list_2717: (42.125000) net_send: could not write to fd=5, errno = 9
bm_list_2717: p4_error: net_send write: -1
p4_error: latest msg from perror: Bad file descriptor
p20_2755: p4_error: net_recv read: probable EOF on socket: 1
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 3198 6542 6543
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
[1] MPI Abort by user Aborting program !
[1] Aborting program!
p1_2718: p4_error: : 1
****************************************************************************************
PanDa
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If your ship doesn't come in, swim out to it.......Jonathan Winters
===================================================================
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
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- application/octet-stream attachment: eqlib.in
- application/octet-stream attachment: eqlib1.in
Received on Sun Apr 01 2007 - 06:07:34 PDT
