[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 13 12:01:43 CEST 2008
There are two potential solutions to this error. For background, refer to:
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
So your options are:
1. If the ligand is present in the .rtp file, make sure your atom nomenclature
corresponds to that of the force field.
2. Remove the ligand and deal with its topology separately (search Google for
John Kerrigan's tutorial for enzyme-ligand systems).
-Justin
vivek sharma wrote:
> Hi Nahren,
> Thanx for your help, I opened the pdb file with swisspdb viewer and then
> tried the pdb2gmx command over that pdb file and got the following error.
>
> Total mass 28295.072 a.m.u.
> Total charge 1.000 e
> Writing topology
> Processing chain 5 'E' (372 atoms, 9 residues)
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Warning: 'NDP' not found in residue topology database, trying to use 'NDPH'
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: pdb2gmx.c, line: 421
>
> Fatal error:
> Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms
> while sorting atoms
> -------------------------------------------------------
>
> and the error for the all atom forcefield were as follow.
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: resall.c, line: 436
>
> Fatal error:
> Residue 'NDP' not found in residue topology database
>
> -------------------------------------------------------
>
>
> any advice for this will be of great help for me.
>
> Thanx,
> Vivek
>
> 2008/8/12 nahren manuel <meetnahren at yahoo.com <mailto:meetnahren at yahoo.com>>
>
> 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
> <mailto:viveksharma.iitb at gmail.com>>/* wrote:
>
> From: vivek sharma <viveksharma.iitb at gmail.com
> <mailto: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
> <mailto: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
> <mailto: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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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