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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>
To: Yang Ye <[EMAIL PROTECTED]>; Discussion list
for GROMACS users <[email protected]>
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 <[EMAIL PROTECTED]> wrote:
Put two semicolon before
;[ defaults ]
;1 1
in the lipid.itp
----- Original Message ----
From: mahbubeh zarrabi <[EMAIL PROTECTED]>
To: [email protected]
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 [email protected]
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
[EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php>
_______________________________________________
gmx-users mailing list [email protected]
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
[EMAIL PROTECTED]
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 [email protected]
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
[EMAIL PROTECTED]
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
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
