[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 15:16:09 CEST 2008



vivek sharma wrote:
> Hi Justin,
> Thanx for your suggestion. But, I am not getting how to do correction in 
> those files I am using gromacs 3.3.3 and 1XU9.pdb molecule for my 
> simulation.
> I am not getting what is happening in the simulation...:(...:(
> kindly suggest.

I'm guessing that NDP is the NADPH cofactor, which in Gromos96 language is 
called NDPH (that's what pdb2gmx is trying to call, it as well).  What's 
happening is you've got the atoms present for NADPH, but the force field simply 
has different names for the atoms.

The simple fix is to re-name the atoms in the .pdb file according to how they 
appear in the .rtp entry for NADPH (called NDPH).  For example, the two 
phosphorus atoms in the phosphodiester between the adenosine and nicotinamide 
moieties are called AP and NP.  AP corresponds to the P atom in the phosphate 
donated by the adenoside system; NP corresponds to the P atom from the 
nicotinamide phosphate.  You've got an atom called PA instead, which is probably 
equivalent to AP (but do check, because that's just a guess from my end).

-Justin

> 
> With Thanx,
> Vivek
> 
> 
> 2008/8/13 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
>     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> <mailto: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>
>            <mailto: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>
>                <mailto: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>
>                <mailto: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>
>                <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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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