FATAL ERROR: Patch needed for tuple is missing

From: rebeca_at_mmb.pcb.ub.es
Date: Wed Aug 13 2008 - 17:31:27 CDT

I am trying to minimize a membrane + protein system composed by DOPC, protein (2
chains), water and ions (Na and Cl). I have constructed the system in GROMACS
(using the amber force field) and then I minimizated it and equilibrated also
in Gromacs.
The equilibrated structure was converted to Amber using the previous parameters
I had used to construct the inverse system, and now I want to simulate this
same system with NAMD, using also the Amber force field.
When I did a minimization (with NAMD/amber) of the water and ions, fixing the
protein and lipids, it went OK, but in the next step, when I removed the
restraints I got already at the beginning very high energies for the bond
energy and it finished with an error of “FATAL ERROR: Patch needed for tuple is

Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
Warning: Bad global bond count!
Warning: Bad global angle count!
Warning: Bad global dihedral count!

ENERGY: 0 99999999.9999 365365.3959 98984.0326 0.0000
 -2167823.2100 123212.5050 0.0000 0.0000 0.0000
99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000


ENERGY: 199 99999999.9999 815179.7216 104931.2051 0.0000
 -2171025.6217 59327748.7788 8406231.4482 0.0000 0.0000
99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000

LDB: LOAD: AVG 83.6608 MAX 88.212 MSGS: TOTAL 1950 MAXC 130 MAXP 1 None
Info: Adjusted background load on 5 nodes.
LDB: LOAD: AVG 83.9996 MAX 100.799 MSGS: TOTAL 2206 MAXC 256 MAXP 1 Alg7
LDB: LOAD: AVG 83.9996 MAX 88.1729 MSGS: TOTAL 2206 MAXC 256 MAXP 1 Alg7
BRACKET: 5.38059e-07 8.87643e+08 -1.45405e+14 -1.39924e+14 -1.31549e+14
Warning: Tuple 711743 with atoms 244971(2079) 244972(2048) missing patch 2048
FATAL ERROR: Patch needed for tuple is missing.

The input I am using is this one (I have tried also to use constraints in the
protein and the lipids, but the error continues):

#protocol parameters
numsteps 5000

cutoff 10
switching off
exclude scaled1-4
1-4scaling 0.833333

#minimization parameters
minimization on
minTinyStep 1.0e-6
minBabyStep 1.0e-2
minLineGoal 1.0e-4

#files de entrada de Amber
amber on
parmfile equilibrado_amber.top
coordinates min1.coor
outputname min2
restartname min2
binaryoutput no
binaryrestart no

constraints on
consref min1_75.pdb
conskfile min1_75.pdb
conskcol B

I think the system is OK because it comes from the equilibration in Gromacs, but
I don´t know what could it be causing this error.

Please, if somebody could help me, it would be really helpful.

Best wishes,

Rebeca Garcia Fandiño
Parc Cientific de Barcelona

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