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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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