Dear Amber friends,
I have done an restraint calculation for umberlla sampling. I use the same input file for AMBER 8 calculation, it works. Howver, a strange error was found when I tried to run in AMBER 10.
======================INPUT FILE========================
Equilibrium MD
&cntrl
imin = 0, irest = 0, ntx = 1, nmropt=1
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 20000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
/
&wt type='DUMPFREQ', istep1=10 /
&wt type='END' /
DISANG=10.restraint
DUMPAVE=10.result
END
===================10.restraint FILE==========================
# distance restrainst
&rst iat=4,5, r1=0.0, r2=10.0, r3=10.0, r4=100.0, rk2 =1.0, rk3 = 1., iresid=1,
ATNAM(1)=P,
ATNAM(2)=N10, ATNAM(2)=N12 /
====================ERROR MESSAGE=========================
p1_5783: p4_error: net_recv read: probable EOF on socket: 1
p2_5809: p4_error: net_recv read: probable EOF on socket: 1
rm_l_1_5806: (0.523438) net_send: could not write to fd=5, errno = 32
p6_5913: p4_error: net_recv read: probable EOF on socket: 1
p7_5939: p4_error: net_recv read: probable EOF on socket: 1
rm_l_6_5936: (0.269531) net_send: could not write to fd=5, errno = 32
rm_l_7_5962: (0.222656) net_send: could not write to fd=5, errno = 32
rm_l_2_5832: (0.472656) net_send: could not write to fd=5, errno = 32
p6_5913: (0.273438) net_send: could not write to fd=5, errno = 32
p4_5861: p4_error: net_recv read: probm_list_5780: (0.582031) wakeup_slave: unable to interrupt slave 0 pid 5779
bm_list_5780: (0.582031) wakeup_slave: unable to interrupt slave 0 pid 5779
==================ERROR MESSAGE 2==============================
PGFIO-F-239/namelist read/unit=33/entity name is not member of group.
File name = 10.restraint formatted, sequential access record = 3
In source file _nmrcal.f, at line number 1345
===============================================================
I double checked that the 3rd line is correct, the residue 4 should have an atom P., residue 5 should have atoms N10 and N12.
Could you please kindly let me know what is wrong here?
By the way, I run the job with /amber10/exe/sander.MPI, is it correct, should I use sander or pnemd instead?
Best regards,
Cat
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Received on Tue May 04 2010 - 04:00:05 PDT
