Re: [gmx-users] atom names do not match

David van der Spoel Thu, 20 Jul 2006 09:33:20 -0700

priyanka srivastava wrote:

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?

Warning: atom names in 96_neatsys14.top and test.gro

In other words: the order of atoms in gro and top is different.
You have to run editconf on the gro file using the index file.

thanks and regards,
Pri...

--- David van der Spoel <[EMAIL PROTECTED]> 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 inthe topology file. you can do that by generating anindex file (manuallyor 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

[EMAIL PROTECTED] [EMAIL PROTECTED]http://folding.bmc.uu.se


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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
[EMAIL PROTECTED]       [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] atom names do not match

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