[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

[nahren manuel]

Dear Vivek,
you just have to download swisspdb and open your pdb file. Thats all you got to do and It is more than enough. If you have more than 2/3 residues missing then, make sure the Ramachandran plots are fine. Also try a simple minimization before begining gromacs.
 
nahren

--- On Tue, 8/12/08, vivek sharma <viveksharma.iitb at gmail.com> wrote:

From: vivek sharma <viveksharma.iitb at gmail.com>
Subject: Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Tuesday, August 12, 2008, 6:34 PM



Hi David,
Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same?
whether swiss pdb can help in such cases?

With Thanx,
Vivek




2008/8/12 David van der Spoel <spoel at xray.bmc.uu.se>




vivek sharma wrote:

Hi There,

I am new to molecular dynamics and GROMACS.
While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command....

 pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce

I got the following in the last of error.....
.......
.......
.......
........
N-terminus: NH3+
C-terminus: COO-
WARNING: atom CE2 not found in residue 270 while adding atom

-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: genhydro.c, line: 304

Fatal error:
Atom CE2 not found in residue PHE270 while adding hydrogens
-------------------------------------------------------
 I tried the same with different force field and water models, but getting the same error again and again.
any suggestion will be highly appreciated.

You have an incorrect pdb file. An atom is missing. You have to fix it yourself.



With thanx,
Vivek

------------------------------------------------------------------------

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