errabah fatima ezzahra wrote:
Hi Justin
when i seperated the NA+ and 6 i got this error
NOTE 1 [file em.mdp]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than rcoulomb.
NOTE 2 [file em.mdp]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than rvdw.
These notes indicate that your .mdp settings are incorrect. Follow the
suggesting printed.
Generated 0 of the 465 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein'
Excluding 1 bonded neighbours molecule type 'W'
Excluding 1 bonded neighbours molecule type 'NA+'
Warning: atom name 3792 in 1pef.top and waterbox_ions.gro does not match
(NA+ - NA)
Warning: atom name 3793 in 1pef.top and waterbox_ions.gro does not match
(NA+ - NA)
Warning: atom name 3794 in 1pef.top and waterbox_ions.gro does not match
(NA+ - NA)
Warning: atom name 3795 in 1pef.top and waterbox_ions.gro does not match
(NA+ - NA)
Warning: atom name 3796 in 1pef.top and waterbox_ions.gro does not match
(NA+ - NA)
Warning: atom name 3797 in 1pef.top and waterbox_ions.gro does not match
(NA+ - NA)
WARNING 1 [file 1pef.top, line 19]:
6 non-matching atom names
atom names from 1pef.top will be used
atom names from waterbox_ions.gro will be ignored
This error is probably harmless, since you are actually using sodium and there
isn't really a mismatch. The name listed in the [molecules] section must match
the name specified in the corresponding [moleculetype] directive in ions.itp,
with constituent residues and atoms named accordingly. In this case, ions.itp
is specifying the atom name as "NA+" while your coordinate file uses "NA" instead.
what s th difference between NA+6 And NA+ 6 .
Spacing. All lines in the [molecules] directive are read as:
(moleculetype name) (some amount of space) (number of molecules)
Proper spacing is an absolute requirement for proper interpretation of the
topology. The amount of whitespace is unimportant, but it has to be there,
otherwise grompp reads a continuous string and finds that there is a
moleculetype named "NA+6" that has no molecules associated with it.
-Justin
------------------------------------------------------------------------
*De :* Justin A. Lemkul <jalem...@vt.edu>
*À :* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Envoyé le :* Mercredi 13 Juillet 2011 13h49
*Objet :* Re: Re : [gmx-users] Adding Ions
Justin A. Lemkul wrote:
>
>
>> i added the NA using the genion
>> *
>>
>> genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the
NA to the topology file , subtracted the water number by 6. tail
waterbox_ions.gro file have this
>> 3567W W 3789 1.256 3.600 3.784
>> 3568W W 3790 2.491 6.539 2.341
>> 3569W W 3791 2.432 6.349 3.116
>> 3570NA NA 3792 2.677 4.903 3.617
>> 3571NA NA 3793 0.466 3.245 4.787
>> 3572NA NA 3794 6.028 4.147 2.550
>> 3573NA NA 3795 3.201 1.027 5.879
>> 3574NA NA 3796 1.677 1.849 6.641
>> 3575NA NA 3797 5.729 5.645 7.089
>> and the topology file
>> #include "martini_v2.1.itp"
>> #include "1pef.itp"
>> #include "martini_v2.0_ions.itp"
>> [ system ]
>>
>> ; Name
>>
>> PEPTIDE F
>>
>> [ molecules ]
>>
>> ; Compound #mols
>>
>> Protein 6
>>
>> W 3551
>>
>> NA+6
>>
>
> This looks fine. There are other things I suggested you look at; you
haven't ruled out that something else went wrong along the way or that
your peptide doesn't have the net charge you think it does.
>
Actually, no it doesn't. You don't have any space between the
moleculetype name ("NA+") and the number of molecules. This line isn't
being read correctly, which might be your problem, though I'm shocked
that you're not getting some other error about a missing number of
molecules or number of coordinates not matching the topology.
-Justin
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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