From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Jan 05 2011 - 08:04:24 CST
There are no parameters in the CHARMM force field for the linkage between
the glucose and acetyl moieties in NAG. Where did you get the topology file
for NAG from? Was there anything else with it?
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Adrian Jasinski
Sent: Wednesday, January 05, 2011 5:36 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: NAG simulation problem with CPS
Hi all
It's my first message so pleas be forgiving for my mistakes and for my
English because it's not very good.
I'm not advance user of NAMD but I also not so newbie.
I tired to do simulation of protein with NAG (stand alone - not connected)
but I have a problem with that and I can't find solution in Internet
and I also don't have anyone who can help me.
when I tired to run NAMD I have error:
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CPS
Fatal error on PE 0> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE
CPS
----------------------------
my psfgen look fine and work without problem (I found in Internet to
replace CPS to CT3):
after that I have another error after runing NAMD:
FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND CT3 - CTS IN PARAMETER
FILES
-------------------
my psfgen file:
topology top_all22_NAG.inp
#topology top_all22_sugar.inp
alias residue HIS HSE
alias atom ILE CD1 CD
alias residue HOH TIP3
alias atom HOH O OH2
alias residue OXY O2
alias residue CPS CT3
segment NAG {
first none
last none
pdb 3KLD_nag1.pdb
}
regenerate angles dihedrals
coordpdb 3KLD_nag1.pdb NAG
writepsf nag1.psf
guesscoord
writepdb nag1.pdb
ENDMOL
-----------------------------------
my input file is like that:
_________________________
structure nag_sc.psf
coordinates nag_sc.pdb
paratypecharmm on
parameters par_all22_sugar.inp
parameters par_all22_prot.inp
#parameters new.par
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8
cutoff 12
pairlistdist 14
margin 0
stepspercycle 20
wrapWater on
rigidBonds water
timestep 1.0
outputenergies 200
outputtiming 200
binaryoutput yes
outputname nag_D0
dcdfreq 100
temperature 300
langevin on
langevinDamping 5
langevinTemp 300
langevinHydrogen no
useFlexibleCell yes
useGroupPressure yes
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp 300
cellBasisVector1 15.732999801635742 0.0 0.0
cellBasisVector2 0.0 19.312999725341797 0.0
cellBasisVector3 0.0 0.0 13.461999893188477
cellOrigin 0.0 0.0 0.0
fixedAtoms on
fixedAtomsFile nag_sc_fix.pdb
fixedAtomsCol O
minimize 100
run 20000
__________________________________
Now I don't know what to do
I would be very grateful for the help and/or advice
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