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

[vivek sharma]

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>

> 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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>>>
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