[gmx-users] Atom index (5) in position_restraints out of bounds (1-4)
pascal.baillod at epfl.ch
pascal.baillod at epfl.ch
Sun Nov 7 23:57:18 CET 2004
Hello,
while using grompp for a topology-file with restrains, I got the following
error-message (genpr was used for the moleculetype MOL, with a force constant of
25000 for every direction):
---------------------------------------------------------------------
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
WARNING 1 [file "ffgro96.itp", line 35]:
Trying to add LJ-14 while the default nonbond type is LJ (SR)
WARNING 2 [file "ffgro96.itp", line 36]:
Trying to add LJ-14 while the default nonbond type is LJ (SR)
WARNING 3 [file "ffgro96.itp", line 37]:
Trying to add LJ-14 while the default nonbond type is LJ (SR)
WARNING 4 [file "ffgro96.itp", line 38]:
Trying to add LJ-14 while the default nonbond type is LJ (SR)
WARNING 5 [file "ffgro96.itp", line 39]:
Trying to add LJ-14 while the default nonbond type is LJ (SR)
WARNING 6 [file "ffgro96.itp", line 40]:
Trying to add LJ-14 while the default nonbond type is LJ (SR)
Generated 148 of the 153 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 153 of the 153 1-4 parameter combinations
Cleaning up temporary file grompphIf3Rz
Fatal error: [ file "posre.itp", line 9 ]:
Atom index (5) in position_restraints out of bounds (1-4)
---------------------------------------------------------------------
while the 6 warnings don't mater (without restrains, grompp runs), I don't know
what this fatal error is about.
question a: how to solve this problem and what means bounds?
here is my ffgro96.itp-file. It is constructed out of a force-field-conversion
amber -> gromacs (1 Komplex containing two molecules which are not bonded with
eachother and one free counterion (Na+)) and the necessary? information about
the solvent (dmso) from the ffgmxnb.itp-file
question b: is there a way to make gromacs accept two .itp-files at the start of
a topology-file?
----------------------------------------------------------------------------
#define _FF_GROMOS
#define _FF_GROMOS96
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
CA 1.00000 0.000 A 0.3399669E+00 0.3598240E+00
CT 1.00000 0.000 A 0.3399669E+00 0.4577296E+00
P 1.00000 0.000 A 0.3741775E+00 0.8368000E+00
O2 1.00000 0.000 A 0.2959922E+00 0.8786400E+00
OS 1.00000 0.000 A 0.3000012E+00 0.7112800E+00
H1 1.00000 0.000 A 0.2471353E+00 0.6568880E-01
HA 1.00000 0.000 A 0.2599642E+00 0.6276000E-01
HC 1.00000 0.000 A 0.2649533E+00 0.6568880E-01
N3 1.00000 0.000 A 0.3249998E+00 0.7112801E+00
OH 1.00000 0.000 A 0.3066473E+00 0.8803136E+00
HO 1.00000 0.000 A 0.0000000E+00 0.0000000E+00
HP 1.00000 0.000 A 0.1959977E+00 0.6568880E-01
H 1.00000 0.000 A 0.0000000E+00 0.0000000E+00
IP 1.00000 0.000 A 0.3328398E+00 0.1158968E-01
SD 32.06000 0.000 A 0.10561E-01 0.21499E-04
OD 15.99940 0.000 A 0.22715E-02 0.75147E-06
CD 15.03500 0.000 A 0.90507E-02 0.21758E-04
[ nonbond_params ]
P OD 1 0.57859E-02 0.40836E-05
CA OD 1 0.15111E-02 0.61175E-06
SD SD 1 0.10561E-01 0.21499E-04
OD OD 1 0.22715E-02 0.75147E-06
CD CD 1 0.90507E-02 0.21758E-04
[ pairtypes ]
SD SD 1 0.10561E-01 0.21499E-04
SD OD 1 0.48978E-02 0.40194E-05
SD CD 1 0.97766E-02 0.21628E-04
OD OD 1 0.22715E-02 0.75147E-06
OD CD 1 0.45341E-02 0.40436E-05
CD CD 1 0.90507E-02 0.21758E-04
-----------------------------------------------------------------------------
and here is my topology-file (I removed all data concerning pairs, bonds, etc to
make it shorter):
------------------------------------------------------------------------------
#include "ffgro96.itp"
[ moleculetype ]
; Name nrexcl
MOL 6
[ atoms ]
1 CA 1 MOL C1 1 -0.3142 12.0100
2 CA 1 MOL C2 2 -0.0768 12.0100
3 CA 1 MOL C3 3 0.0329 12.0100
4 CA 1 MOL C4 4 -0.1694 12.0100
5 CA 1 MOL C5 5 0.0329 12.0100
6 CA 1 MOL C6 6 -0.0768 12.0100
7 CT 1 MOL C7 7 -0.1555 12.0100
8 P 1 MOL P1 8 1.1043 30.9700
9 O2 1 MOL O1 8 -0.8155 16.0000
10 CT 1 MOL C8 9 -0.1555 12.0100
11 P 1 MOL P2 10 1.1043 30.9700
12 O2 1 MOL O2 10 -0.8155 16.0000
13 O2 1 MOL O3 11 -0.8155 16.0000
14 OS 1 MOL O4 11 -0.4802 16.0000
15 CT 1 MOL C9 12 -0.0321 12.0100
16 OS 1 MOL O5 13 -0.4802 16.0000
17 O2 1 MOL O6 13 -0.8155 16.0000
18 CT 1 MOL C10 14 -0.0321 12.0100
19 H1 1 MOL H1 15 0.0581 1.0080
20 HA 1 MOL H2 16 0.1298 1.0080
21 HA 1 MOL H3 17 0.1257 1.0080
22 HA 1 MOL H4 18 0.1353 1.0080
23 HA 1 MOL H5 19 0.1257 1.0080
24 H1 1 MOL H6 20 0.0581 1.0080
25 H1 1 MOL H7 20 0.0581 1.0080
26 HC 1 MOL H8 21 0.0237 1.0080
27 HC 1 MOL H9 21 0.0237 1.0080
28 HC 1 MOL H10 22 0.0237 1.0080
29 HC 1 MOL H11 22 0.0237 1.0080
30 H1 1 MOL H12 23 0.0581 1.0080
31 H1 1 MOL H13 23 0.0581 1.0080
32 H1 1 MOL H14 23 0.0581 1.0080
[moleculetype]
MOM 6
[moleculetype]
Na+ 0
[atoms]
1 IP 1 Na+ Na+ 1 1.0000 22.9900
#include "dmso.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
[ system ]
; Name
Complex in dmso
[ molecules ]
; Compound #mols
MOL 1
MOM 1
Na+ 1
DMSO 450
------------------------------------------------------------------------------
many thanks
Pascal Baillod
*******************************************************************************
Pascal Baillod (PhD student)
*******************************************************************************
Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry pascal.baillod at epfl.ch
Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch
CH-1015 Lausanne
*******************************************************************************
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