[gmx-users] g_x2top is missing bonds

[Justin Lemkul]

On 1/31/13 4:10 PM, Matt Watkins wrote:
> Oops. Well, I'd be interested in people's opinions and don't intend to hijack
> FX's thread.
>
> I do use the code regularly and greatly appreciate all the effort that people
> have put into its development. But, particularly, the inability to easily mix
> buckingham and lennard-jones is awkward for easily mixing inorganic/organic
> systems.
>
> Apologies again to those offended, and maybe it could be a useful discussion,
>

Feature requests are always welcome on redmine.gromacs.org.  In the past 7 or so 
years of reading this list, I can count on one hand the amount of times people 
have asked about mixing Buckingham and LJ interactions, if that gives you any 
idea.  Either people who want it are very quiet, or there's not a very 
persistent need for such features.  The core development team only implements 
what they feel is generally useful or has been necessary for their own work. 
There is only so much time to get all these things done, and version 4.6 IMHO 
represents a heroic amount of effort given all the new toys we have to play 
with.  If people have useful contributions for various features, they are always 
welcome.  Gromacs is open-source for a reason :)

Gromacs was indeed built around biomolecular simulations, but I have seen people 
do rather elegant and creative work with other systems.  Any time I do anything 
particularly crafty, I write a tutorial ;)  Gromacs is very user-driven.

We are on our way to version 5.0, which will likely represent significant change 
to just about everything.  If there are features you want (or even better, are 
willing to help develop), Redmine is the place to file away wishlists, and the 
gmx-developers mailing list is the appropriate forum to talk about code.

-Justin

> On Thu, 31 Jan 2013 19:32:36 -0000, FX <fxcoudert at gmail.com> wrote:
>
>> Hello,
>>
>> I'm trying to prepare a MD of a hybrid organic-inorganic crystal, i.e. only
>> one big molecule extending throughout space with PBC. I have prepared my .gro
>> file from the PDB (and checked it with babel/vmd). I'm trying to generate the
>> topology with g_x2top. I have:
>>
>>   - created a directory for my forcefield
>>   - suitable atomname2type.n2t in there
>>   - forcefield.itp file with my bonded forcefield parameters
>>
>> However, g_x2top complains about not finding the expected number of bonds:
>>
>>> g_x2top -f zif8.gro -o topol.top -ff myff -name test -pbc
>>> Fatal error:
>>> Could only find a forcefield type for 240 out of 276 atoms
>>
>>
>> The weird part is: all zinc atoms should be equivalent, so there is no reason
>> for some to have 2 or 3 bonds while the others have 4 (as expected). Given
>> that the .gro file is correct (including PBC), where could the problem come
>> from? And how to diagnose it further?
>>
>> Thanks in advance for any hint, and apologies if I've not given enough
>> information (or too much).
>>
>> Sincerely,
>> FX
>>
>>
>> PS: I don't know what's the policy on this list, so in doubt I attach the
>> directory with my files
>>
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>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================