[gmx-users] atom names do not match

[priyanka srivastava]

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


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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