Anna Marabotti wrote:
Dear all,
as requested, I'm copying here the SDS.itp file (it should be not too big):
; This file was generated by PRODRG version AA081006.0504
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comme
Dear all,
as requested, I'm copying here the SDS.itp file (it should be not too big):
; This file was generated by PRODRG version AA081006.0504
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to d...@davapc1.bioch.
Anna Marabotti wrote:
[ moleculetype ]
; Name nrexcl
SDS 3
; Include topology for SDS
#include "SDS.itp"
Isn't this moleculetype already specified within SDS.itp? Perhaps posting the
contents of SDS.itp will help solve this issue; the rest of the topology seems
fine, except this
Dear all,
thank you for continuous support. Here briefly what I made:
1) I deleted SDS from the first [moleculetype] section of the old .top file =
doesn't work
2) I added a new [moleculetype] section after #include "ions.itp", followed by
#include "SDS.itp" (just before
[ system ] and [ molecul
Thomas Schlesier wrote:
Hi,
i think another problem lies here:
; Include water topology
#include "spc.itp"
.
; Include generic topology for ions
#include "ions.itp"
; Include topology for SDS
#include "SDS.itp"
[ system ]
; Name
Protein in water with SDS
[ molecules ]
; Co
hich the species appear in
the [ molecules ] section.
-Justin
Thomas
--
Message: 5
Date: Wed, 17 Jun 2009 09:11:29 -0400
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Re: protein in SDS/water
To: Discussion list for GROMACS users
Message-ID: <4a3
SDS - water; but these
two orders must be the same.
-> Delete the line, which Justin suggested und put the *#include
"SDS.itp"* before the *#include "spc.itp"*, then i think all must be fine.
Thomas
>
>
> --------------
>
> Message: 5
&g
Anna Marabotti wrote:
Dear Mark,
thank you very much for suggestions. I'm pasting here an "extract" of the .top
file I used during the grompp
process (the complete one is too big to be sent to the mailing list, as I told
yesterday - the dots indicate
that I delete the information here, but they
Anna Marabotti wrote:
Dear Mark,
thank you very much for suggestions. I'm pasting here an "extract" of the .top
file I used during the grompp
process (the complete one is too big to be sent to the mailing list, as I told
yesterday - the dots indicate
that I delete the information here, but th
Dear Mark,
thank you very much for suggestions. I'm pasting here an "extract" of the .top
file I used during the grompp
process (the complete one is too big to be sent to the mailing list, as I told
yesterday - the dots indicate
that I delete the information here, but they are present in the orig
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