[gmx-users] pdb2gmx problem

[K.A. Feenstra]

alexander yakovenko wrote:
> 
> Hi All,
> I have the next problem. I try to make the topology of the nonprotein
> molecule with 143 atoms. I found that pdb2gmx add some bonds which
> were not stored in rtp file, and some atoms leave separate. I check
> the topology manually (rtp file) and haven t fount any separated atoms
> in rtp.
> Why pdb2gmx add and remove some bonds automatically?

AFAIK, pdb2gmx only takes bond information fom the .rtp and it will
not add any additional ones or remove some. pdb2gmx usually also
prints quite a number of helpful messages and errors. One guess I
could make is that you may have two atoms with the same name in
your .rtp entry; this is not allowed and will cause undefined
behavior.

> Is my molecule too large?

There are no size limits to molecules in Gromacs.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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