Dear Amber Developers,
I'm running targeted MD with a small protein of ~6k atoms(H added). Here is my input file:
targeted MD tgtfitmask
&cntrl
imin = 0, ntx = 5, nstlim = 600000, irest = 1,
dt = 0.002, ntc = 2, ntf = 2,
temp0 = 300.0,
cut = 8.0,
ntpr = 4000, ntwx = 5000, ntwr = 20000,
ntb = 2, ntt = 3, ntp = 1,
igb = 0, nmropt = 1, gamma_ln = 2.0,
tgtfitmask = ":22-25,112-116.CA",
itgtmd = 1, tgtmdfrc = 3,
tgtrmsmask = ":1-4,355-358,11,12,13,343,344,166-174.CA | :345,346 &",
/
&wt
TYPE = 'TGTRMSD', istep1 = 1, istep2 = 500000,
value1 = 8.0, value2 = 0.0,
/
&wt
TYPE = 'TGTRMSD', istep1 = 500001, istep2 = 600000,
value1 = 0.0, value2 = 0.0,
/
&wt
type = "END",
In the output file I get the following error:
defa
Mask ":22-25,112-116.CA" matches 9 atoms
Error in group input::atommask.f::pop_evalstack
stack underflow
I've reduced the number of atoms but it came out just the same error. And, in another case of a protein of 20k atoms, the targeted MD worked well with exactly the same parameters and the tgtfitmask is: tgtfitmask = ":490,870,47,669,769,567,869,872,892,891,495,894,409,665,900,798,388,871,61,489,630,893,791,631,795,881,778,576,883,793,788,799,584,336,758,797,182,767,581,26,158,796,347,656,677,695,681,660,675,694,8,190,671,794,252,354,10.CA"
Are there any problems with the input parameters? Do I need to modified the related source code? By the way, I couldn't find the file atommask.f in amber18.
Best,
Yao Li
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Received on Mon Aug 27 2018 - 00:30:03 PDT
