Hello,
I think you got that error message because in the lipid.itp the interaction
parameters between the lipid atoms and the gromos atoms are from the
ffgmxnb.itp (see the begining of lipid.itp). But for you it is irrelevant,
because you have only POPC and water in your system. (so the line
Shalom Pragya,
I wonder if the 'grompp' program finished properly after it gives you
this message? If not, please send the command you used and the output
you got from it.
Best,
Itamar
pragya chohan wrote:
hi i m pragya, i found this article i used ffG43a1 and got this
error when ran
hi i m pragya, i found this article i used ffG43a1 and got this error when
ran grompp:
Atomtype 'CA' not found! . i m using popc128a.pdb from tieleman site and m
using "lipid.itp"
#include "ffG43a1.itp"#include "lipid.itp"#include "popc.itp"
#ifdef FLEX_SPC#include "flexspc.itp"#else#incl
fcyfcz
>>>11 1000 1000 1000
>>> #endif
>>> ; Include generic topology for ions
>>> #include "ions.itp"
>>> [ system ]
>>> ; Name
>>> protein and POPC
>>> [ molecules ]
>>> ; Comp
11 1000 1000 1000
>>> #endif
>>> ; Include generic topology for ions
>>> #include "ions.itp"
>>> [ system ]
>>> ; Name
>>> protein and POPC
>>> [ molecules ]
>>> ; Compound#mols
>&
tp"
[ system ]
; Name
protein and POPC
[ molecules ]
; Compound#mols
Protein_X1
POP 489
Regards,
Yang Ye
- Original Message
From: mahbubeh zarrabi <[EMAIL PROTECTED]>
To: Yang Ye <[EMAIL PROTECTED]>; Discussion list
for GROMACS users
Sent: Monday, May
system ]
> ; Name
> protein and POPC
> [ molecules ]
> ; Compound#mols
> Protein_X1
> POP 489
>
> Regards,
> Yang Ye
>
> - Original Message
> From: mahbubeh zarrabi <[EMAIL PROTECTED]>
> To: Yang Ye <[EMAIL P
ons
#include "ions.itp"
[ system ]
; Name
protein and POPC
[ molecules ]
; Compound#mols
Protein_X1
POP 489
Regards,
Yang Ye
- Original Message
From: mahbubeh zarrabi <[EMAIL PROTECTED]>
To: Yang Ye <[EMAIL PROTECTED]>; Discussion list for GROMACS users
ahbubeh zarrabi <[EMAIL PROTECTED]>
> To: gmx-users@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
&
Put two semicolon before
;[ defaults ]
;1 1
in the lipid.itp
- Original Message
From: mahbubeh zarrabi <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Monday, May 28, 2007 4:41:19 PM
Subject: [gmx-users] simulation popc
Dear all
I want to simulate protein in
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 rega
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