[gmx-users] chargegroups????????

[David]

On Sat, 2005-09-03 at 16:57 +0530, Rahul Karyappa wrote:
> Dear all,
>       I am new to Gromacs. Since one nomth I am trying to run my
> models on Gromacs. But I am not 100% successeful. Using PRODRG website
> I am able to crate .gro and .top files and also I am able to run MD
> run on them. But when create them using gromacs commands I am still
> not successful. I think I am making  mistakes while  defining the .rtp
> parameters. My partial .pdb file looks like this:
>  
> REMARK   4 Poly COMPLIES WITH FORMAT V. 2.0 
> HETATM    1  HT  PAA     1      -0.423   6.910  -1.504  1.00  0.00
> H  
> HETATM    2  C1  PAA     1       0.155   6.563  -2.363  1.00  0.00
> C  
> HETATM    3  C2* PAA     1       1.609   6.203  -1.930  1.00  0.00
> C  
> HETATM    4  C3  PAA     1       1.609   5.131  -0.899  1.00  0.00
> C  
> HETATM    5  O1  PAA     1       1.237   3.954  -1.147  1.00  0.00
> O1-
> HETATM    6 2HC  PAA     1       2.037   7.095  -1.462  1.00  0.00
> H  
> HETATM    7 1H1C PAA     1      -0.339   5.686  -2.789  1.00  0.00
> H  
> HETATM    8 1H2C PAA     1       0.157   7.352  -3.119  1.00  0.00
> H  
> HETATM    9  O2  PAA     1       2.122   5.306   0.227  1.00  0.00
> O  
> HETATM   10 NA10 PAA     2       3.217   2.864  -0.095  1.00  0.00
> NA1+
> This in one repeat unit of the polymer surrounded by sodium ions.
> While including the atoms in the .rtp file I am including them for one
> repeat unit. But when I run pdb2gmx it says there are missing atoms. I
> think while mentioning the charge group I am making mistake. I have
> given 1 as a charge group for the atoms and 2 for sodium ion. But
> chargegroup are different for remaining repeat units. Is this the
> problem or anything else is there? Do I need to specify atosm for all
> the repeat units?

Don't put the Na+ in the rtp since it is not covalently bound. pdb2gmx
probably complanis about the termini: run with flag -ter and select None
for N- and C-terminus.


> please help me out?
> Thanking you in advance. please answer this question. It's very
> important  for me.
> 
> Rahul Karyappa
> NCL, India
> 
> 
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-- 
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://xray.bmc.uu.se/~spoel
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