[gmx-users] Fatal error: No molecule were defined in the system
Repic Matej
matej.repic at epfl.ch
Mon Aug 31 12:39:12 CEST 2015
This is only the include topology, but the functional topology for grompp
needs a few more lines. Make another file such as below and this should
run fine through grompp, provided you have a big enough box defined in
5-fu.gro. Note that this will run the 5-FU dynamics in the gas phase,
since there are no water molecules in the topology, nor the necessary
parameters are included to use water. There must be water in the 5-fu.gro
coordinate file as well, of course.
----------------main.top---------------------
[ defaults ]
1 2 yes 0.5 0.8333
#include 5-fu.itp
[ system ]
; Name
5-fluorouracil
[ molecules ]
UNK 1
----------------main.top---------------------
Best,
Matej
------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------
On 8/31/15, 12:10, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Mehrnoosh Hazrati"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
mehrnoosh.hazrati at modares.ac.ir> wrote:
>Dear all,
>
>hi,
>
>I'm simulating the drug "5-Flouorouracil", since its topology file is not
>available, I've written it by hand.
>But I got the error "No molecule were defined in the system" when run
>grompp.
>where could be the problem?
>
>Thank you in advance.
>
>Regards,
>Mehrnoosh
>
>The .itp file is attached below:
>
>
>[ moleculetype ]
>; Name nrexcl
>UNK 3
>
>[ atoms ]
>; nr type resnr resid atom cgnr charge mass
> 1 opls_719 1 UNK F 0 -0.325 18.9984
> 2 opls_328 1 UNK O 1 -0.567 15.9994
> 3 opls_326 1 UNK O 2 -0.613 15.9994
> 4 opls_321 1 UNK N 3 -0.641 14.0067
> 5 opls_319 1 UNK N 4 -0.603 14.0067
> 6 opls_322 1 UNK C 5 +0.602 12.0110
> 7 opls_320 1 UNK C 6 +0.805 12.0110
> 8 opls_718 1 UNK C 7 +0.275 12.0110
> 9 opls_324 1 UNK C 8 -0.005 12.0110
> 10 opls_327 1 UNK H 9 +0.424 1.0079
> 11 opls_327 1 UNK H 10 +0.421 1.0079
> 12 opls_330 1 UNK H 11 +0.227 1.0079
>; total charge of the molecule: 0.000
>[ bonds ]
>; ai aj funct c0 c1
> 1 8 1 1.33863 323004.8
> 2 6 1 1.21616 476976.0
> 3 7 1 1.21609 476976.0
> 4 6 1 1.40749 349782.4
> 4 7 1 1.39161 349782.4
> 4 10 1 1.01427 363171.2
> 5 7 1 1.39060 349782.4
> 5 9 1 1.38105 357313.6
> 5 11 1 1.01039 363171.2
> 6 8 1 1.46503 392459.2
> 8 9 1 1.34636 392459.2
> 9 12 1 1.08322 307105.6
>
>[ angles ]
>; ai aj ak funct c0 c1 c2 c3
> 1 8 6 1 117.02620 585.760
> 1 8 9 1 121.35396 585.760
> 2 6 4 1 122.04483 669.440
> 2 6 8 1 125.88929 669.440
> 3 7 4 1 124.02387 669.440
> 3 7 5 1 123.24541 669.440
> 4 6 8 1 112.06588 585.760
> 4 7 5 1 112.73072 585.760
> 5 9 8 1 120.66155 585.760
> 5 9 12 1 117.10729 418.400
> 6 4 7 1 128.91643 585.760
> 6 4 10 1 115.76471 418.400
> 6 8 9 1 121.61985 527.184
> 7 4 10 1 115.31885 418.400
> 7 5 11 1 115.20972 418.400
> 8 9 12 1 122.23116 418.400
> 9 5 11 1 120.78471 418.400
>
>[ dihedrals ]
>; improper dihedral
>; ai aj ak al func t0 k
> 4 6 7 10 2 0.0 167.36
> 5 9 7 11 2 0.0 167.36
> 6 4 8 2 2 0.0 167.36
> 7 4 5 3 2 0.0 167.36
> 8 9 6 1 2 0.0 167.36
> 9 5 8 12 2 0.0 167.36
>[ dihedrals ]
>; ai aj ak al func t0 k mult
> 1 8 6 4 1 180.0 41.80 2
> 2 6 4 7 1 180.0 41.80 2
> 3 7 4 6 1 180.0 41.80 2
> 4 7 5 11 1 180.0 41.80 2
> 7 5 9 12 1 180.0 41.80 2
> 8 9 5 11 1 180.0 41.80 2
>--
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