On Thu, Nov 01, 2007 at 12:36:33PM +, Moutusi Manna wrote:
> Hi
> I want to perform peptide + popc membrane simulation. I download
> popc128a.pdb from
> (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
> Before I introduce the peptide into the membrane, the wate
>> Hi
>> I want to perform peptide + popc membrane simulation. I download
>> popc128a.pdb from
>>
>> (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
>> Before I introduce the peptide into the membrane, the water layer
>> had to be broadened to ensure full so
[EMAIL PROTECTED] wrote:
Hi
I want to perform peptide + popc membrane simulation. I download
popc128a.pdb from
(http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
Before I introduce the peptide into the membrane, the water layer
had to be broadened to ensure full
Hi
I want to perform peptide + popc membrane simulation. I download
popc128a.pdb from
(http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
Before I introduce the peptide into the membrane, the water layer
had to be broadened to ensure full solvation of the peptid
Hi
I want to perform peptide + popc membrane simulation. I download
popc128a.pdb from
(http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
Before I introduce the peptide into the membrane, the water layer had to be
broadened to ensure full solvation of the peptide .I i
thanks for reply.I want to perform simulation of popc membrane.
Steps which i have done are as follows:
1. download popc128a.pdb, popc.it,lipids.itp
(http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
2. download ffgmx_lipids files
3.convert POPC of .top & popc.itp
Quoting Moutusi Manna <[EMAIL PROTECTED]>:
> thanks for reply.I want to perform simulation of popc membrane.
> Steps which i have done are as follows:
> 1. download popc128a.pdb, popc.it,lipids.itp
> (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
> 2. download ff
thanks for reply.I want to perform simulation of popc membrane.
Steps which i have done are as follows:
1. download popc128a.pdb, popc.it,lipids.itp
(http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
2. download ffgmx_lipids files
3.convert POPC of .top & popc.itp i
Hi all,I had similar problem with Fatal errors with Atomtype LC3 not found while setting up a POPC simulation. After a day of trying out different things I figured out the problem. And I would like to share my experience in the mailing list. Renaming of POP to POPC in the .gro files doesn't matter.
Hi All,thanks to Steffan , Jim and Kaushal for helping me out in the POPC simulation setup. i finally got everything to work. i guess the imp thing was to change the POPC to POP in .top file. thanks once again.Arindam Ganguly
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gmx-users mailing list
I previously posted my modifications to get POPE to work with OPLSAA. You could
make the analogous changes to your system. The message was:
[gmx-users] lipid.itp LJ-1,4 values involving water
Wed May 3 20:44:51 CEST 2006
___
gmx-users mailing listgm
0 0.201000
1646 1 0.450 0.451000
At the and of 50 ps bd simulation from lambda=0 to lambda=1 distance
between 23 and 46 atoms increased from 0.196 to 0.448 nm, and
distance
between 16 and 46 atoms increased form 0.496 to 0.73 nm.
Can anyone suggest, why
da=1 distance
between 23 and 46 atoms increased from 0.196 to 0.448 nm, and distance
between 16 and 46 atoms increased form 0.496 to 0.73 nm.
Can anyone suggest, why results of fep are so strange? Is this a bug
or I'm missing something?
P.S. I run all these tests with gromacs 3.3.1
---
Arindam,
I fixed this problem a while ago and it was pretty difficult to
figure out. I tinkered with so many things, once I got it to work I
didn't even know what steps I took to fix it!
Here's something to try: GROMACS doesn't like the fact popc.itp has
a four-character residue name (si
Hi Steffen,
thanks for the reply. this is what i have done. my topol.top looks
like this now
#inlcude ffgmx.itp
inlcude popc.itp.
as per your last reply i have copied the contents of lipid.itp to
ffgmxbon.itp and ffgmxnb.itp without removing the contents of the
respective file. basically just app
Arindam Ganguly wrote:
Hi Steffen,
Thanks very much for the prompt reply. i made the changes as mentioned
such that my popc.top looks like this :-
#include "ffgmx.itp"
#include "lipid.itp"
#include "popc.itp"
#include "ffgmx2nb.itp"
#include "ffgmx2bon.itp"
however is still get the same messag
Hi Steffen,Thanks very much for the prompt reply. i made the changes as mentioned such that my popc.top looks like this :-#include "ffgmx.itp"#include "lipid.itp"#include "popc.itp"
#include "ffgmx2nb.itp"#include "ffgmx2bon.itp"however is still get the same message "Fatal error: Bonded/nonbonded a
Hi Arindam,
you've simply got to switch two lines in the *.top file: lipid.itp has
to be called by the topology before popc.itp, as it contains the
information on atomtypes for GROMACS. So:
#include "lipid.itp"
#include "popc.itp"
should work just fine.
Greetings
Steffen
--
Dipl.-Chem. Steff
Hi gmx-users,i am trying to run a POPC simulation. this is what i have done. i downloaded the popc128apdb, lipid.itp , popc.itp files from the following website
http://moose.bio.ucalgary.ca/index.php?page=Downloads then i also downloaded the ffgmx_lipids files from the gromacs website.i have copie
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