[gmx-users] error while running pdb2gmx....

Rahul Karyappa r.karyappa at ncl.res.in
Wed Aug 31 14:02:06 CEST 2005

Dear all,

    Hi I am running a mdrun on one polymer chain. I have
entered all the atoms and atom types in .rtp file. But while running
pdb2gmx command it gives one error that atom O is not entered in the
.rtp file. Actually there are two O atoms which are given in .pdb as
O1- and O2. I have mentioned the same atoms. But it asks for O atom
which is not there in the .pdb file. What should I do? Where am I going

  In the .rtp file I have mentioned atoms for only one repeat
unit. Is it Ok or do I need to specify all the atoms for all the repeat
units? Because when I run pdb2gmx it gives me warnging that several
atoms are missing. How do I enter chargegroup because in the .pdb file
chargegroup no. is different for different repeat unit. PLease tell me
about this.

   Thanking you in advance. looking forward to your kind reply.

Rahul Karyappa

NCL, Pune

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