[gmx-users] CNT

[Dallas Warren]

The warning is due to having the molecules in the topology .top file
listed in a different order to how they appear in the coordinate file,
.gro


The list within the topology has to be in the same order, even if you
have broken up groups of the same molecules in the coordinate file.

 

As for the error.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of trevor brown
Sent: Thursday, 20 January 2011 10:51 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] CNT

 

Hi Justin,

I added lines to ffnonbonded.itp. It resulted in following error. It has
some warnings and an error. I am interested in error. After that I will
look at the warnings. In which file we may have an error? It is not
specified.

 

best wishes

trevor

 

 

Generated 335790 of the 335790 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 335790 of the 335790 1-4 parameter combinations
Excluding 5 bonded neighbours molecule type 'ICE'
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
Warning: atom name 170 in topol.top and final2.gro does not match (H1 -
CA)
Warning: atom name 171 in topol.top and final2.gro does not match (H2 -
C)
Warning: atom name 172 in topol.top and final2.gro does not match (H3 -
O)
Warning: atom name 173 in topol.top and final2.gro does not match (CA -
CB)
Warning: atom name 174 in topol.top and final2.gro does not match (HA -
CG)
Warning: atom name 175 in topol.top and final2.gro does not match (CB -
CD1)
Warning: atom name 176 in topol.top and final2.gro does not match (HB1 -
CD2)
Warning: atom name 177 in topol.top and final2.gro does not match (HB2 -
HA)
Warning: atom name 178 in topol.top and final2.gro does not match (CG -
HB1)
Warning: atom name 179 in topol.top and final2.gro does not match (HG -
HB2)
Warning: atom name 180 in topol.top and final2.gro does not match (CD1 -
HG)
Warning: atom name 184 in topol.top and final2.gro does not match (CD2 -
HD21)
Warning: atom name 185 in topol.top and final2.gro does not match (HD21
- HD22)
Warning: atom name 186 in topol.top and final2.gro does not match (HD22
- HD23)
Warning: atom name 187 in topol.top and final2.gro does not match (HD23
- H1)
Warning: atom name 188 in topol.top and final2.gro does not match (C -
H2)
Warning: atom name 189 in topol.top and final2.gro does not match (O -
N)
Warning: atom name 190 in topol.top and final2.gro does not match (N -
CA)
Warning: atom name 191 in topol.top and final2.gro does not match (H -
C)
Warning: atom name 192 in topol.top and final2.gro does not match (CA -
O)
(more than 20 non-matching atom names)

WARNING 2 [file topol.top, line 39]:
  184 non-matching atom names
  atom names from topol.top will be used
  atom names from final2.gro will be ignored

 

There were 2 warnings

-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: grompp.c, line: 1356

Fatal error:
There was 1 error in input file(s)

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