[gmx-users] Atomtype:CB

[Justin Lemkul]

Quoting pkmukher <pkmukher at olemiss.edu>:

> Hello users,
>
>   I found a problem similar to one described in the mailing
> list. The problem occurs in grompp wherein it says
> unrecognized atom type CB. As suggested in the mailing list
> the problem arises when in a ligand protein system the
> ligand is prepared using the PRODRG server GROMOS87 format
> and the protein is prepared in some other FF..in my case
> 43a1(GROMOS96)..when i prepared my protein using the -ff gmx
> flag (gmx Gromacs Forcefield (a modified GROMOS87)) grompp
> did not have any problems. My question is that is there a
> way to prepare the ligand in 43a1 format so that when i run
> grompp the relevant input files are is the same desired
> format. Thanks in advance

I believe the PRODRG beta server provides parameters compatible with Gromos96
43a1.

-Justin

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Justin A. Lemkul
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu
(540) 231-9080

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