[gmx-users] Question

[Justin Lemkul]

On 10/23/12 2:18 AM, Davoud Zare wrote:
> Dear Sir
> I am a newbie on Gromacs. I am trying to solvate my protein (1CJ5.pdb) with water. I am following the tutorial by Justin Lemkul but when I execute the following command
> pdb2gmx -f 1CJ5.pdb -o 1CJ5_processed.gro -water spce
>
> and choose OPLS-AA/L all-atom force field
> I am getting an fatal error
> Fatal error:
> Atom HB3 in residue TYR 2 was not found in rtp entry TYR with 21 atomswhile sorting atoms.
> any comments on that?

http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry

Either rename your hydrogen atoms to conform to the expectations of the force 
field or use -ignh to allow pdb2gmx to build what it needs.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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