[gmx-users] atom names do not match

[priyanka srivastava]

Dear Sir, 
thank you so much for your reply.
I made the index.ndx file and ran grompp with the
index file that I have made, but with no change and I
still get the same mesg.
I just hope I have understood your suggestion
correctly. Which manual sorting are we talking about?
What exactly is the problem?

thanks and regards,
Pri...

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> priyanka srivastava wrote:
> > Thanks again for your kind response.
> > 
> > I guess I will write down my problem once again
> :-)
> > 
> > I am trying to study a pure bilayer system for
> which I
> >  am interested in running the production run using
> > gromacs. I already have the system with me i.e. a
> pdb
> > file after the minimization and all the
> constraints
> > etc.
> > 
> > Now what I am intersted in doing is, I want to run
> the
> > production run ONLY using gromacs.
> > 
> > So, My starting point is a pdb file containing
> only
> > the DMPC residues.
> > 
> > The steps that I am following are as follows:
> > 
> > 1. Generate a .top file from  the information
> > available on Peter Tielemann's website i.e. by
> using
> > lipid.itp, dmpc.itp. The identifier used for water
> is
> > SOL though the water present in my original pdb
> file
> > is TIP3.
> > 
> > 2. I am unable to use pdb2gmx since it gives me
> the
> > error:
> > "residue DMPC is not present in residue topology
> > database"
> > 
> > 3. So, I use editconf to make the .gro file 
> > 
> > 4. Then I am adding the box-dimensions using
> editconf
> > once again.
> > 
> > 5. Now when I run grompp after this using the .top
> > file that I have made (from the website) and the
> .gro
> > (from editconf) I get the following mesg:
> > 
> > 
> > calling /lib/cpp...
> > processing topology...
> > Generated 1369 of the 2211 non-bonded parameter
> > combinations
> > Excluding 3 bonded neighbours for DMPC 96
> > Excluding 2 bonded neighbours for SOL 2866
> > processing coordinates...
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (CN1 - NC3)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (CN2 - C13)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (CN3 - C14)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (NTM - C15)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (CA - C12)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (CB - C11)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (OA - PO4)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (P - O13)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (OB - O14)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (OC - O11)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (OD - O12)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (CC - C1)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (CD - C2)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (OE - O21)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (C2A - C21)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (OF - O22)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (C2B - C22)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (C2C - C3)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (C2D - O31)
> > Warning: atom names in 96_neatsys14.top and
> test.gro
> > don't match (C2E - C31)
> > (more than 20 non-matching atom names)
> > WARNING 1 [file "96_neatsys14.top", line 20]:
> >   13014 non-matching atom names
> >   atom names from 96_neatsys14.top will be used
> >   atom names from test.gro will be ignored
> 
> 
> you should probably sort the coordinates of the
> lipids to match that in 
> the topology file. you can do that by generating an
> index file (manually 
> or with a script that you write).
> 
> 
> > 
> > 
> > When I look at the atom types that are there in
> the
> > .gro file they seem to be the problem, i.e. the
> > choline Nitrogen is represented as N only which
> refers
> > to a peptide N in gromacs. What should I do?
> > Please help me and also suggest me if I am going
> in
> > the right direction or not?
> > 
> > eagerly waiting for the gromacs experts response,
> > warm regards,
> > Pri...
> > 
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> 
> -- 
> David.
>
________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://folding.bmc.uu.se
>
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