[gmx-users] nucleic acis simulation

[Erik Marklund]

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 Lombardia wrote:
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> David van der Spoel escribió el 28/02/06 11:25 :
>> Miguel Ortiz Lombardia wrote:
>> Thank you Maik.
>>
>> The AMBER ports are some I'm testing, sure.
>> BTW, I can't get it ready if I solvate the model. Everything goes fine
>> until grompp complains:
>>
>> $> grompp -v -f em -c watered -o em -p nucT
>>
>> (...)
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 3.3
>> Source code file: toppush.c, line: 1108
>>
>> Fatal error:
>> [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:
>>              Atom index (1) in settles out of bounds (1-0)
>> -------------------------------------------------------
>>
>> Any clues of what may be wrong?
>>
>>> order of bits in the topology file. chpater 5
> 
> The order of the elements in the topology file seem the same whether
> this is created using ffG43a1 or ffamber99. However, only the second
> prompts the error at the grompp step. I read the topology and
> molecule.itp file formats in chapter 5 of the manual (v. 3.2), but I was
> not able to spot the problem. Could you please be more precise?
> 
> Thank you!
> 
> 
> Miguel
> - --
> 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
> email: molatwork at yahoo.es
> www: http://www.ysbl.york.ac.uk/~mol/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Je suis de la mauvaise herbe,
> Braves gens, braves gens,
> Je pousse en liberté
> Dans les jardins mal fréquentés!
>                                                        Georges Brassens
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the position in the top file where the spc.itp was included is wrong.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se