Dear Amber Users,
I have run into an issue trying to apply a dihedral restraint between four
centers of mass (each defined by a group of atoms), and running a short
test trajectory using PMEMD implemented in Amber 16.
I have been able to get a successful run using sander, however, I would
like to make this work (if possible) using PMEMD to take advantage of GPU
acceleration.
The error I get when I run PMEMD is:
forrtl: severe (19): invalid reference to variable in NAMELIST input, unit
33, file ~/temp/test.restraint, line 31, position 6
Image PC Routine Line Source
libifcore.so.5 00002B5D547248BD for__io_return Unknown Unknown
libifcore.so.5 00002B5D5476F015 for_read_seq_nml Unknown Unknown
pmemd 0000000000574CC6 Unknown Unknown Unknown
pmemd 00000000005B3F7F Unknown Unknown Unknown
pmemd 000000000040A299 Unknown Unknown Unknown
pmemd 00000000004045A8 Unknown Unknown Unknown
pmemd 00000000004044AE Unknown Unknown Unknown
libc.so.6 00002B5D566142E0 __libc_start_main Unknown Unknown
pmemd 00000000004043AA Unknown Unknown Unknown
Here is my input file:
test:
&cntrl
imin = 0, irest = 1, ntx = 5,
ntb = 2, pres0 = 1.0, ntp = 1,
ig=-1, ioutfm=1,
iwrap=1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2, ntb=2,
tempi = 310.0, temp0 = 310.0,
ntt = 3, gamma_ln = 3.0,
nstlim = 1, dt = 0.001,
ntpr = 1, ntwx = 1, ntwr = 1,
nmropt=1,
/
&end
&wt
type='DUMPFREQ', istep1=1
&end
&wt
type='END',
&end
DISANG=test.restraint
DUMPAVE=temp_info.dat
Here is my restraint file (test.restraint):
# test run
&rst
iat=-1,-1,-1,-1, iresid=1,
r1=-180, r2=0, r3=0, r4=180,
rk2=10, rk3=10,
igr1= 215,215,215,215,215,215,229,229,229,229,229,229,229,229,229,0,
grnam1(1)=N1,
grnam1(2)=C2,
grnam1(3)=N3,
grnam1(4)=C4,
grnam1(5)=C5,
grnam1(6)=C6,
grnam1(7)=N1,
grnam1(8)=C2,
grnam1(9)=N3,
grnam1(10)=C4,
grnam1(11)=C5,
grnam1(12)=C6,
grnam1(13)=N7,
grnam1(14)=C8,
grnam1(15)=N9,
igr2= 215,216,216,216,216,0,
grnam2(1)=O3',
grnam2(2)=P,
grnam2(3)=OP1,
grnam2(4)=OP2,
grnam2(5)=O5',
igr3= 215,215,215,215,214,0,
grnam3(1)=O5',
grnam3(2)=P1,
grnam3(3)=O1P,
grnam3(4)=O2P,
grnam3(5)=O3',
igr4= 215,215,215,215,215,215,0,
grnam4(1)=N1,
grnam4(2)=C2,
grnam4(3)=N3,
grnam4(4)=C4,
grnam4(5)=C5,
grnam4(6)=C6,
&end
/
Any help would be greatly appreciated,
Stefan
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Received on Fri Mar 02 2018 - 16:00:01 PST
