Hello,
I'm trying to run mdgx with a blocked dipeptide. I've done this
successfully before, but now the program runs for about two seconds then
fails with the following error message:
CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
CreateBellyMask >> controls a constraint group and is mobile, but
CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
CreateBellyMask >> constraint group, is not mobile.
CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
CreateBellyMask >> controls a constraint group and is mobile, but
CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
CreateBellyMask >> constraint group, is not mobile.
CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
CreateBellyMask >> controls a constraint group and is mobile, but
CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
CreateBellyMask >> constraint group, is not mobile.
CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
CreateBellyMask >> controls a constraint group and is mobile, but
CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
CreateBellyMask >> constraint group, is not mobile.
CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
CreateBellyMask >> controls a constraint group and is mobile, but
CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
CreateBellyMask >> constraint group, is not mobile.
CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
CreateBellyMask >> controls a constraint group and is mobile, but
CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
CreateBellyMask >> constraint group, is not mobile.
CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
CreateBellyMask >> controls a constraint group and is mobile, but
CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
CreateBellyMask >> constraint group, is not mobile.
CreateBellyMask >> Error. Atom 6 (residue AIB 1 N )
CreateBellyMask >> controls a constraint group and is mobile, but
CreateBellyMask >> atom 1 (residue ACE 0 CH3 ), part of the
CreateBellyMask >> constraint group, is not mobile.
I don't know what this means.
Here's my mdgx input script (the &cntrl portion):
&cntrl
imin = 0
irest = 0
dt = 0.002
nstlim = 250000
ntp = 0
ntt = 3
tempi = 298.0
temp0 = 298.0
gamma_ln = 1.0
* rigidbond = 1*
rigidwat = 1
es_cutoff = 10.0
vdw_cutoff = 10.0
ntpr = 500
ntwr = 250000
ntwx = 500
iwrap = 1,
&end
If I remove the rigidbond =1 line it runs just fine. However, I would like
to keep that in.
I have attached my (solvated) topology and coordinate files and the full
mdgx input for reference.
Thanks,
AB
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Received on Mon Apr 15 2019 - 08:00:04 PDT
