CHARMM27 or CHARMM36 doesn't make different for me. I just want to get a good
output of simulation.
Before this, Justin also suggested me for CHARMM36. Ok, I will use CHARMM36.
But about the atom types, it's not still clear for me what I need to do. If I
use the CHARMM36, am I supposed to build berger lipids?
Thanks,
Shima
________________________________
From: Anirban <reach.anirban.gh...@gmail.com>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>
Sent: Friday, May 11, 2012 8:58 PM
Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
On Fri, May 11, 2012 at 9:13 PM, Shima Arasteh <shima_arasteh2...@yahoo.com>
wrote:
Dear Anirban,
>No, I have not done. Because I didn't know I need Berger lipids for this
>simulation.
>
Actually I think the coordinate and topology files from Tieleman's site are in
accordance with the Berger lipid parameters and hence works with the
united-atom gromos FF. You can also get CHARMM27 lipids from
http://terpconnect.umd.edu/~jbklauda/research/download.html here. And the
atom-type errors can be solved if you can build a proper .hdb file with the
proper corrections for the violating atom names.
-Anirban
Thanks for you reply,
>Cheers,
>Shima
>
>
>
>
>________________________________
> From: Anirban <reach.anirban.gh...@gmail.com>
>To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS
>users <gmx-users@gromacs.org>
>Sent: Friday, May 11, 2012 8:10 PM
>Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
>
>
>
>
>
>
>On Fri, May 11, 2012 at 7:36 PM, Shima Arasteh <shima_arasteh2...@yahoo.com>
>wrote:
>
>Dear gmx users,
>>
>>
>>I'm going to simulate the POPC in water.
>>I downloaded required files in Tielman site and made the .top file. Then
>>included the CHARMM27.ff in the .top file.
>>When I run the grompp I get the fatal error as below:
>>Atomtype CB not found
>>
>>
>>
>>I have done the same with gromos87.ff . But I didn't see any error.
>>What's the problem?
>>Anybody may suggest me how to solve this problem? Is this because of the
>>forcefield? Or something in .top file goes wrong?
>>
>>
>
>Have properly edited the CHARMM27 bonded and nonbonded .itp files to include
>the Berger lipid parameters and have you included the POPC topology? You can
>follow this tutorial to get an idea:
>
>https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
>
>-Anirban
>
>Thanks,
>>Shima
>>
>>--
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>
>
>
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