[gmx-users] Re: gmx-users Digest, Vol 69, Issue 123

[Vitaly V. Chaban]

> You said before:
>
> "> > 5. What does your .top look like? (does it list the organic molecule
>  > > only once in the [ molecules ] section?)
>
> Only once."
>

OK. We misunderstood one another. I meant "CIP is mentioned only once"
= "one string with CIP molecules number". So this entry was not really
duplicated.


> Does this mean you have only one solute?  Or that you have only one entry for
> solute, which you then have multiple molecules of in the system?  There
> certainly can be confusion if you aren't describing your system clearly.
>
> The reason for asking is that the problematic atom numbers (which are greater
> than 42, as Chris pointed out) would indicate one of two possibilities:
>
> 1. CIP is present multiple times, and one of those molecules (at least) is
> having a problem.

YES. I just need to find out why the problem appears.