[gmx-users] Fatal error:No molecules were defined in the system

[Nilesh Dhumal]

I tried to send whole file.


File is big. Can I forward to your personal email directly?



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    Re: [gmx-users] Fatal error:No molecules were defined in the
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>
> On 10/20/14 11:19 AM, Nilesh Dhumal wrote:
>> Hello,
>>
>> For grompp
>>
>> grompp -f minim_hy.mdp -c cu.gro -p test.top -o 1.tpr
>>
>> I get the error" Fatal error:No molecules were defined in the system"
>>
>> Here I pasted initial part of test.top file.
>>
>>
>>
>>
>> ; Derived from parsing of runfiles/alat.top.orig
>> [ defaults ]
>> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>>   1               3               yes             0.5     0.5
>> ; comb-rule 3 is square-root sigma, the OPLSAA version
>>
>> [ atomtypes ]
>> ; full atom descriptions are available in ffoplsaa.atp
>> ; name  bond_type    mass    charge   ptype          sigma      epsilon
>>   opls_991   Cu    29	63.54600    1.098       A    3.114e-01
>> 0.02092e+00
>>   opls_993   OA    8     15.99940    -0.665       A    3.033e-01
>> 0.401664e+00
>>   opls_994   OB    8     15.99940    -0.665       A    3.033e-01
>> 0.401664e+00
>>   opls_995   CA    6     12.0110      0.778       A    3.473e-01
>> 0.39748e+00
>>   opls_996   CB    6     12.0110     -0.092       A    3.473e-01
>> 0.39748e+00
>>   opls_997   CC    6     12.0110     -0.014       A    3.473e-01
>> 0.39748e+00
>>   opls_998   HM    1      1.0080      0.109       A    2.846e-01
>> 0.06276e+00
>>
>> [ moleculetype ]
>> ; Name            nrexcl
>>   BTC             3
>>
>> [ atoms ]
>> ;   nr       type  resnr residue  atom   cgnr     charge       mass
>> typeB
>>     chargeB      massB
>>    1    opls_993      1    BTC    OA       1    -0.665    15.99940
>>    2    opls_995      1    BTC    CA       2     0.778    12.01100
>>    3    opls_996      1    BTC    CB       3    -0.092    12.01100
>>    4    opls_997      1    BTC    CC       4    -0.014    12.01100
>>    5    opls_998      1    BTC    HM       5     0.109     1.00800
>>    6    opls_997      1    BTC    CC       6    -0.014    12.01100
>>    7    opls_998      1    BTC    HM       7     0.109     1.00800
>>    8    opls_993      1    BTC    OA       8    -0.665    15.99940
>>    9    opls_995      1    BTC    CA       9     0.778    12.01100
>>   10    opls_996      1    BTC    CB      10    -0.092    12.01100
>>   11    opls_997      1    BTC    CC      11    -0.014    12.01100
>>   12    opls_998      1    BTC    HM      12     0.109     1.00800
>>   13    opls_993      1    BTC    OA      13    -0.665    15.99940
>>   14    opls_995      1    BTC    CA      14     0.778    12.01100
>>   15    opls_996      1    BTC    CB      15    -0.092    12.01100
>>   16    opls_994      1    BTC    OB      16    -0.665    15.99940
>>   17    opls_994      1    BTC    OB      17    -0.665    15.99940
>>   18    opls_994      1    BTC    OB      18    -0.665    15.99940
>>   19    opls_993      1    BTC    OA      19    -0.665    15.99940
>>   20    opls_995      1    BTC    CA      20     0.778    12.01100
>>
>> Is there any error in .top file?
>>
>
> There is no way to tell unless you provide the full file.  Either there is
> a
> syntax error somewhere that breaks the parsing, or your [molecules]
> section is
> empty.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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