[gmx-users] problem with pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 21 13:34:31 CEST 2011

Saurav Saha wrote:
> 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.

You need an intact model to start with.  There are no Gromacs tools to 
reconstruct missing atoms (aside from H, which is handled by the .hdb file if 
necessary).  You'll have to use external software to model in the missing atom 
before you can proceed.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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