[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens
vivek sharma
viveksharma.iitb at gmail.com
Wed Aug 13 15:04:59 CEST 2008
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.
With Thanx,
Vivek
2008/8/13 Justin A. Lemkul <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>>
>>
>> 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
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list.
>> Use the www interface or send it to
>> gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search
>> before posting!
>> Please don't post (un)subscribe requests to the list. Use
>> the www interface or send it to
>> gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
>>
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org <mailto:
>> gmx-users at gromacs.org>
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org <mailto:
>> gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080813/715df9e0/attachment.html>
More information about the gromacs.org_gmx-users
mailing list