[gmx-users] nucleic acis simulation

Miguel Ortiz-Lombardia molatwork at yahoo.es
Tue Nov 14 15:10:52 CET 2006

Hi Erik,

Yep, the problem was indeed with the ifdefs... I'm sorry, I thought I
had posted a solution. My bad.


En/na Erik Marklund ha escrit:
> Hi everyone.
> I found this old thread and noticed that Miguel Ortis Lombardia had the
> same problems I had just half an hour ago. It seems that it is indeed
> the included spc.itp that causes the problem, but NOT the position where
> it is included as David van der Spoel suggests. A closer look at spc.itp
> (or in my case spce.itp) reveals that the [ atoms ] section is stuffed
> with preprocessor conditionals defining spc building blocks in various
> ways depending on the force field at hand. If AMBERXX is used, the
> [ atoms ] section is skipped all together. After adding a new chunk of
> code to the [ atoms ] section in my own copy of spce.itp everything
> worked smoothly:
> #ifdef _FF_AMBER99 
>      1  amber99_54 1    SOL     OW      1    -0.8476   15.99940
>      2  amber99_55 1    SOL    HW1      1     0.4238    1.00800
>      3  amber99_55 1    SOL    HW2      1     0.4238    1.00800
> #endif
> I got the atom types from ffamber03.rtp and most of the other stuff from
> other parts of spce.itp. NOTE: do make sure that the masses and charges
> are correct if you attempt this approach. Don't copy the values above if
> using regular spc.
> /Erik

Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: molatwork at yahoo.es
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