[gmx-users] coordinates don't match

Lalita Shaki lalitashaky at gmail.com
Wed Aug 27 12:13:43 CEST 2014

Hi Lovika,

If the coordinates do not match it usually means you have more molecules in
your pdb file than in the top. It will be easier to know which is the
problem if you tell us which is the system and how the top file look like.



> Hi everyone ,
> I have a question , If coordinates of my .pdb file and .top file are not
> matching than what is the right way to correct it ! Like if I have one
> coordinate more in .pdb than in .top and I delete one  from .pdb ...and it
> get fine !!! Will it be a problem in future or its fine to do this ?? Is
> there any other way to correct it ...without deleting !!
> Thanks and Regards
> Lovika
Lalita S. Uribe.
European Master in Theoretical Chemistry and Computational Modeling.
PhD student. Johannes Gutenberg-Universität Mainz

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