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

[Rahul Karyappa]

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?

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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