[gmx-users] atom names do not match

[David van der Spoel]

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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