Dear User,
I am trying to run MD (sander serial) with protein-miRNA and mRNA complex
with tleap input:
source leaprc.protein.ff19SB
source leaprc.RNA.OL3
loadOff terminal_monophosphate.lib
source leaprc.water.tip3p
designed = loadPdb 2032.amber-2.pdb
check designed
addions designed Na+ 4
solvateOct designed TIP3PBOX 9.00 0.75
charge designed
saveAmberParm designed 2032.prm.top 2032.prm.crd
savepdb designed 2032.out.pdb
quit
warnings are:
home/researchscholler/AMBER/amber20_src/bin/teLeap: Warning!
There is a bond of 5.736 angstroms between C and N atoms:
------- .R<GLY 67>.A<C 6> and .R<LYS 68>.A<N 1>
/home/researchscholler/AMBER/amber20_src/bin/teLeap: Warning!
There is a bond of 7.456 angstroms between C and N atoms:
------- .R<PRO 97>.A<C 13> and .R<ILE 98>.A<N 1>
/home/researchscholler/AMBER/amber20_src/bin/teLeap: Warning!
There is a bond of 6.297 angstroms between C and N atoms:
------- .R<CYS 243>.A<C 10> and .R<LYS 244>.A<N 1>
/home/researchscholler/AMBER/amber20_src/bin/teLeap: Warning!
There is a bond of 5.725 angstroms between C and N atoms:
------- .R<PRO 570>.A<C 13> and .R<LYS 571>.A<N 1>
/home/researchscholler/AMBER/amber20_src/bin/teLeap: Note.
Ignoring the warnings from Unit Checking.
proceeding with these warnings for minimization with input :
&cntrl
imin=1, maxcyc=10000,ncyc= 5000, cut=8.0, igb=0, ntb=1, ntp=0, ntpr=100,
/
I obtained TOTAL SIZE OF NONBOND LIST = 19504477.
further proceeding for MD with input file:
&cntrl
imin = 0,
ntx = 5, irest = 1,
ntpr = 500, ntwr = 1000, ntwx = 500, ntwe = 500, iwrap = 1
ntf = 2, igb = 0,
cut = 10.0,
nstlim = 5000, dt = 0.002,
tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
ntb = 2, ntp = 1, taup = 1.0
ntc = 2, tol = 0.00001,
vlimit = -1.0d0,
ioutfm=1,
/
&ewald
vdwmeth = 1,
/
I get the error:
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x7F5DD55F66D7
#1 0x7F5DD55F6D1E
#2 0x7F5DD4DF344F
#3 0x49AE44 in __nblist_MOD_grid_ucell
#4 0x49F193 in __nblist_MOD_nonbond_list
#5 0x597F19 in force_
#6 0x62A6B9 in runmd_
#7 0x5E19D2 in sander_
#8 0x5DA874 in MAIN__ at multisander.F90:?
./md.sh: line 65: 21802 Segmentation fault (core dumped)
I am not able to resolve the problem.
Regards,
Richa
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 17 2021 - 00:00:02 PDT
