Date: Wed, 9 Oct 2024 15:47:36 +0000
Dear Amber users and developers,
I tried to simulate dissociation of protein-protein complex (594aa and 252aa residues) using GaMD (Amber24, ff19SB and OPC3)
and made the setup according to manual, but immediately after launch the following error occurred:
terminate called after throwing an instance of 'std::runtime_error'
what(): Too many TI atoms--current limit: 500 atoms
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x145700b1c960 in ???
#1 0x145700b1bac5 in ???
#2 0x14570091351f in ???
#3 0x1457009679fc in ???
#4 0x145700913475 in ???
#5 0x1457008f97f2 in ???
#6 0x145700e76b9d in ???
#7 0x145700e8220b in ???
#8 0x145700e82276 in ???
#9 0x145700e824d7 in ???
#10 0x558b9c2bf227 in ???
#11 0x558b9c4d56f6 in ???
#12 0x558b9c389b62 in ???
#13 0x558b9c2bfbfe in ???
#14 0x1457008fad8f in ???
#15 0x1457008fae3f in ???
#16 0x558b9c2db9f4 in ???
#17 0xffffffffffffffff in ???
here is my mdin file:
500 ns NVT GaMD PP
&cntrl
irest = 1, ntx = 5, ig = -1,
nstlim=250000000,dt=0.002,
ntc= 2,ntf= 2,
cut=9.0, ntb=1, ntp=0,
ntwx=10000, ntwr = 10000,
ntt=3, gamma_ln=2.0,
temp0=300.0,ioutfm=1,iwrap=1,
ntpr = 2000,
icfe = 1, ifsc = 1,gti_cpu_output = 0,gti_add_sc = 1,
timask1 = ':1-594', scmask1 = ':1-594',
bgpro2atm=9547,edpro2atm=13658,
timask2 = '', scmask2 = '',
igamd = 16, iE = 1, iEP = 1, iED = 1, irest_gamd = 0,
ntcmd = 1000000, nteb = 1000000, ntave = 50000,
ntcmdprep = 200000, ntebprep = 200000,
sigma0P = 6.0, sigma0D = 6.0,
/
The example here https://www.med.unc.edu/pharm/miaolab/resources/gamd/tutorial/
has 110aa residues which buy the way should also exceed 500 atoms.
Do you have any ideas how to overcome this, please?
Kind regards
Nick
Computational chemistry and
molecular modeling
The Nancy and Stephen Grand Israel National Center for Personalized Medicine
Weizmann Institute of Science
M +972 52 7439671
234 Herzl Street, P.o. Box 26,
Rehovot, 7610001 Israel
[1694421514730]
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/png attachment: OutlookEmoji-16944215147305d29569d-dcd2-4a3a-8ae5-bf4608de3a11.png)
