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

Vitaly V. Chaban vvchaban at gmail.com
Sun Jan 24 19:59:53 CET 2010

> 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

> 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.

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