<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">You shall read up manual for the structure of topology file.</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">For your problem, you shall create a top file which contains</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">#include "ffgmx.itp"<BR>#include "lipid.itp"<BR>#include "popc.itp"</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">#include "prox.itp"<BR>#ifdef POSRES<BR>; #include "prox-posre-100000.itp"<BR>#include "prox-posre.itp"<BR>#endif</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">#include "spc.itp"<BR>#ifdef POSRES_WATER<BR>; Position restraint for each water oxygen<BR>[ position_restraints ]<BR>; i funct fcx fcy fcz<BR> 1 1 1000 1000 1000<BR>#endif</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">; Include generic topology for ions<BR>#include "ions.itp"</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">[ system ]<BR>; Name<BR>protein and POPC</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">[ molecules ]<BR>; Compound #mols<BR>Protein_X 1<BR>POP 489<BR></DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Regards,</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Yang Ye</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"> </DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: mahbubeh zarrabi <zarrab_m@yahoo.com><BR>To: Yang Ye <leafyoung@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org><BR>Sent: Monday, May 28, 2007 7:56:23 PM<BR>Subject: Re: [gmx-users] simulation popc<BR><BR>
<DIV>dear freind<BR>thanks for helping. there is another errore: no such<BR>moleculetype protein.<BR>best wishes<BR>--- Yang Ye <leafyoung@yahoo.com> wrote:<BR><BR>> Put two semicolon before<BR>> <BR>> ;[ defaults ]<BR>> ;1 1<BR>> <BR>> in the lipid.itp<BR>> <BR>> ----- Original Message ----<BR>> From: mahbubeh zarrabi <zarrab_m@yahoo.com><BR>> To: gmx-users@gromacs.org<BR>> Sent: Monday, May 28, 2007 4:41:19 PM<BR>> Subject: [gmx-users] simulation popc<BR>> <BR>> <BR>> Dear all<BR>> I want to simulate protein in popc.I dowanload<BR>> popc128a.pdb from tieleman site and insert protein<BR>> in<BR>> popc by VMD BUT I can not run grompp.there is<BR>> errore:<BR>> found a second defaults directive file ffgmx.itp<BR>> line6.whould you please help me?which protocole is<BR>> useful for me(in detail)?<BR>> best regard<BR>> <BR>> <BR>> <BR>>
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