[gmx-users] problem with pdb2gmx

Saurav Saha sauravsaha at ymail.com
Wed Sep 21 12:14:47 CEST 2011

Dear Everyone,

I am Saurav B. Saha from India. I am newbie to gromacs. I am interested in using gromacs for ligand receptor interaction. But when i started my first step by using "pdb2gmx -f structure.pdb -water tip3p" i am getting fatal error (Fatal error:Atom CD not found in residue seq.nr. 7 while adding atom
) and from error report when i checked my pdb file i did not find any REMARK 465 in my pdb file however, in REMARK 470 i got MISSING ATOM report. I am using protein structure which has been elucidated my wet lab. Kindly help.
I dont understand where to begin with.

Thanks in advance.

Saurav B. Saha

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