[gmx-users] grompp , lipid parameters, error

[Pedro Alexandre Lapido Loureiro]

Citando Senthil Kandasamy <senthilk at engin.umich.edu>:

> Hi all,
> 
> I am still having some difficulties with grompp and tieleman's lipid.itp
> file.
> 
> First, I added the 11 atomtypes into the ffgmxnb.itp . then i added the
> nonbonded parameters and so on....
> 
> then I added the dihedral lines to ffgmxbon.itp
> 
> I think that I did these things correctly. I am pretty sure about this.
> This allows me to get rid of the lipid.itp file.
> 
> Now,my simulation topology file looks as follows
> 
> #include ffgmx.itp
> #include pope.itp
> #include spc.itp
> #include magain-nh.itp
> 
> [system]
> pope + water +magainin 
> 
> [molecules]
> POPE 256
> SOL  8429
> Protein 1
> 
> now i run 
> 
> grompp -appropriate options,
> 
> I get 
> calling /lib/cpp...
> processing topology...
> fatal error: Atomtype 'LNL'  not found.
> 
> I do not understand why this happens since atomtype LNL is defined in
> ffgmx.itp. I had added the 11 new atomtypes from lipid.itp (of which LNL
> is one) right behind the default 47 atomtpyes in ffgmx.
> 
> and btw, LNL is the first "non-default" residue grompp comes across in
> the input gro file.
> 
> I do not know if I am doing something obviously wrong...
> something to do with the order of file inclusions?
> I have tried a whole bunch of things only get even more complicated
> errors.
> any ideas?
> 
> Senthil
> 

Hello Senthil,

you have also to add the 11 atom types to ffgmx.atp!
Have you done this?

Cheers, 

Pedro.



--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil