[gmx-users] atoms

Dinesh Pinisetty dpinis1 at lsu.edu
Tue Jul 27 21:55:54 CEST 2004

Hi all,
    I mean what does atom typr 'LO' or 'LOM' stand for.In DPPC we have
CH2,CH3,P,N,O atom types when i have seen its structure but in Dr.Tielman's
site I have downloaded lipid.itp and dppc.itp files wherein we have 12 atom
types like 'LO' 'LOM' 'LC3' 'LC2' etc.Full form means,I does not mean
charges,bond types etc I need what exactly they stand for.As a very
beginner I just want to understand atom types present in the file
properly.When I see DPPC structure I have seen 5-6 atom types but in the
file I have 12 atom types or so.
  Please tell me what they stand for and why there is a difference in the
atom types between the structure and in the file.
I hope you got what I mean.Thanks a lot in advance..........

From:gmx-users-bounces at gromacs.org on 07/26/2004 05:41 PM ZE2

Sent by: gmx-users-bounces at gromacs.org

Please respond to Discussion list for GROMACS users <gmx-users at gromacs.org>

To:   Discussion list for GROMACS users <gmx-users at gromacs.org>
cc:   (bcc: Dinesh Pinisetty/dpinis1/LSU)

Subject:    Re: [gmx-users] atoms

Dinesh Pinisetty wrote:
> Hi all,
>     Could anyone please tell me where I can get the full forms of all the
> atomtypes used in pdb files and .itp files.If suppose I want to know the
> full form of atomtypes 'LO' or 'LOM' or 'CA' etc which are present in the
> lipid.itp files of Dr.Tielmans website,where should I refer to.

What do you mean by 'full form'? The [atomtypes] section defines the mass,
LJ parameters and charge. What else is there to know?


_____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

gmx-users mailing list
gmx-users at gromacs.org
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list