[gmx-users] Regarding genconf

[jani vinod]

Thanks for reply ,The problem is solved .The problem was with topology file
.

On Fri, Jun 4, 2010 at 4:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> jani vinod wrote:
>
>> Hello,
>> I build a system solvated in water .
>> Then replicated the system using genconf. Now when I am running grompp i
>> am
>> getting following warning
>> Warning: atom name 404 in PH7.top and replicate_systemB.gro does not match
>> (N - C1)
>> Warning: atom name 405 in PH7.top and replicate_systemB.gro does not match
>> (H1 - C2)
>> Warning: atom name 406 in PH7.top and replicate_systemB.gro does not match
>> (H2 - C3)
>> Warning: atom name 407 in PH7.top and replicate_systemB.gro does not match
>> (H3 - N4)
>> Warning: atom name 408 in PH7.top and replicate_systemB.gro does not match
>> (CA - C5)
>> Warning: atom name 409 in PH7.top and replicate_systemB.gro does not match
>> (CB - C6)
>> Warning: atom name 410 in PH7.top and replicate_systemB.gro does not match
>> (CG - O7)
>> Warning: atom name 411 in PH7.top and replicate_systemB.gro does not match
>> (OD1 - P8)
>> Warning: atom name 412 in PH7.top and replicate_systemB.gro does not match
>> (OD2 - O9)
>> Warning: atom name 413 in PH7.top and replicate_systemB.gro does not match
>> (C - O10)
>> Warning: atom name 414 in PH7.top and replicate_systemB.gro does not match
>> (O - O11)
>> Warning: atom name 415 in PH7.top and replicate_systemB.gro does not match
>> (N - C12)
>> Warning: atom name 416 in PH7.top and replicate_systemB.gro does not match
>> (H - C13)
>> Warning: atom name 417 in PH7.top and replicate_systemB.gro does not match
>> (CA - O14)
>> Warning: atom name 418 in PH7.top and replicate_systemB.gro does not match
>> (CB - C15)
>> Warning: atom name 419 in PH7.top and replicate_systemB.gro does not match
>> (C - O16)
>> Warning: atom name 420 in PH7.top and replicate_systemB.gro does not match
>> (O - C17)
>> Warning: atom name 421 in PH7.top and replicate_systemB.gro does not match
>> (N - C18)
>> Warning: atom name 422 in PH7.top and replicate_systemB.gro does not match
>> (H - C19)
>> Warning: atom name 423 in PH7.top and replicate_systemB.gro does not match
>> (CA - C20)
>>
>> and when after ignoring the warning I try to run system my system get
>> distorted.
>>
>>
> Whenever grompp throws warnings like this, don't ignore them and plow
> ahead, it's a recipe for disaster.  The [molecules] section of your topology
> is out of order with respect to your coordinate file, so parameters for
> different species are being applied incorrectly.
>
> -Justin
>
>
>> Thanks
>> vinod
>>
>>
> --
> ========================================
>
> 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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