NAG simulation problem with CPS

From: Adrian Jasiñski (adrian_at_fizyka.umk.pl)
Date: Wed Jan 05 2011 - 05:36:00 CST

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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