FATAL ERROR: Patch needed for tuple is missing

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

Hello,
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
missing”:

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!
ETITLE: TS BOND ANGLE DIHED IMPRP
         ELECT VDW BOUNDARY MISC KINETIC
        TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG

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

#nonbonded
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
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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:45 CST