[gmx-users] simulation popc

[Yang Ye]

On 5/28/2007 9:23 PM, mahbubeh zarrabi wrote:
> Dear yang
> thanks very much.the some of atomes do not
> found(NR,CH,N5,...).they are in lipid.itp
>   
Didn't get what you mean? Any other problems?

Regards,
Yang Ye
> best wishes
> --- Yang Ye <leafyoung at yahoo.com> wrote:
>
>   
>> You shall read up manual for the structure of
>> topology file.
>>
>> For your problem, you shall create a top file which
>> contains
>>
>> #include "ffgmx.itp"
>> #include "lipid.itp"
>> #include "popc.itp"
>> #include "prox.itp"
>> #ifdef POSRES
>> ; #include "prox-posre-100000.itp"
>> #include "prox-posre.itp"
>> #endif
>> #include "spc.itp"
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct       fcx        fcy        fcz
>>    1    1       1000       1000       1000
>> #endif
>> ; Include generic topology for ions
>> #include "ions.itp"
>> [ system ]
>> ; Name
>> protein and POPC
>> [ molecules ]
>> ; Compound        #mols
>> Protein_X            1
>> POP 489
>>
>> Regards,
>> Yang Ye
>>
>> ----- Original Message ----
>> From: mahbubeh zarrabi <zarrab_m at yahoo.com>
>> To: Yang Ye <leafyoung at yahoo.com>; Discussion list
>> for GROMACS users <gmx-users at gromacs.org>
>> Sent: Monday, May 28, 2007 7:56:23 PM
>> Subject: Re: [gmx-users] simulation popc
>>
>>
>> dear freind
>> thanks for helping. there is another errore: no such
>> moleculetype protein.
>> best wishes
>> --- Yang Ye <leafyoung at yahoo.com> wrote:
>>
>>     
>>> Put two semicolon before
>>>
>>> ;[ defaults ]
>>> ;1       1
>>>
>>> in the lipid.itp
>>>
>>> ----- Original Message ----
>>> From: mahbubeh zarrabi <zarrab_m at yahoo.com>
>>> To: gmx-users at gromacs.org
>>> Sent: Monday, May 28, 2007 4:41:19 PM
>>> Subject: [gmx-users] simulation popc
>>>
>>>
>>> Dear all
>>> I want to simulate protein in popc.I dowanload
>>> popc128a.pdb from tieleman site and insert protein
>>> in
>>> popc by VMD BUT I can not run grompp.there is
>>> errore:
>>> found a second defaults directive file ffgmx.itp
>>> line6.whould you please help me?which protocole is
>>> useful for me(in detail)?
>>> best regard
>>>
>>>
>>>
>>>
>>>
>>>       
> ____________________________________________________________________________________
>   
>>> Bored stiff? Loosen up... 
>>> Download and play hundreds of games for free on
>>> Yahoo! Games.
>>> http://games.yahoo.com/games/front
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/search before posting!
>>> 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>
>> _______________________________________________
>>     
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/search before posting!
>>> 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
>>
>>
>>
>>
>>
>>
>>     
> ____________________________________________________________________________________
>   
>> Need Mail bonding?
>> Go to the Yahoo! Mail Q&A for great tips from Yahoo!
>> Answers users.
>>
>>     
> http://answers.yahoo.com/dir/?link=list&sid=396546091>
> _______________________________________________
>   
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/search before posting!
>> 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
>
>
>
>        
> ____________________________________________________________________________________Luggage? GPS? Comic books? 
> Check out fitting gifts for grads at Yahoo! Search
> http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz
>
>