[gmx-users] Regarding KALP-15 Simulation

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:
> Dear All,
>              *Sorry folks* without following the subsequent lines I came 
> to wrong conclusion. But I got stuck with some other problem. After 
> concatenating the dppc128 periodicity corrected box and kalp box the 
> numbers indices of the atoms are not continuos so when I run the grompp 
> command I am getting an error. Is there any easy way to correct those 
> numbers in an easy way.
> 

What error are you getting?  The numbering in the .gro file should not cause a 
problem.  Non-consecutive numbering in the .top can cause a fatal error, but 
should not be relevant here.

-Justin

> I am showing part of the final gro file to  explain my problem clearly
>   16ALA     CA  132   3.227   3.454   4.449
>    16ALA     CB  133   3.160   3.571   4.374
>    16ALA      C  134   3.130   3.393   4.550
>    16ALA      O  135   3.149   3.408   4.670
>    17NH2      N  136   3.044   3.305   4.501
>    17NH2     H1  137   3.046   3.283   4.404
>   * 17NH2     H2  138   2.978   3.261   4.561**
>     1DPPC    C1    1   1.577   5.265   0.920*
>     1DPPC    C2    2   1.675   5.295   1.135
>     1DPPC    C3    3   1.648   5.482   0.985
>     1DPPC    N4    4   1.680   5.338   0.995
>     1DPPC    C5    5   1.808   5.301   0.932
>     1DPPC    C6    6   1.929   5.396   0.953
> 
> Thank you in Advance.
> 
> *With Regards,
> Ravi Kumar Venkatraman,
> IPC Dept., IISc,
> Bangalore, INDIA.
> 
> +91-9686933963.*
> 

-- 
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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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