[gmx-users] atom names do not match

[David van der Spoel]

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 <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...
>>>
>>>__________________________________________________
>>>Do You Yahoo!?
>>>Tired of spam?  Yahoo! Mail has the best spam
>>
>>protection around 
>>
>>>http://mail.yahoo.com 
>>>_______________________________________________
>>>gmx-users mailing list    gmx-users at gromacs.org
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>>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
>>
>>
>>-- 
>>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
>>
> 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>>_______________________________________________
>>gmx-users mailing list    gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>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
>>
> 
> 
> 
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around 
> http://mail.yahoo.com 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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


-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++