[gmx-users] Simulation of POPC in water using CHARMM27

[Shima Arasteh]

OK, I'll give it a try.
Thank you again! :-)

Cheers,
Shima



________________________________
 From: Anirban <reach.anirban.ghosh at gmail.com>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, May 11, 2012 9:22 PM
Subject: Re: [gmx-users] Simulation of POPC in water using CHARMM27
 




On Fri, May 11, 2012 at 10:08 PM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:

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?
>
>
 
Actually if you use CHARMM36 FF then no need to use Berger parameters, since CHARMM36 FF already have the all-atom POPC parameters. But there are differences among the atom types. So you can use these POPC files (Peter Lai provided me these files and these were generated for the following work: (please reference):
Lai, P.C. and Crasto, C.J.
Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
Front. Gene.
Volume 3 Year 2012 Number 61
DOI: 10.3389/fgene.2012.00061) 
 
These files worked fine for me (with grompp). Include the popc.itp file in your .top file.
 
-Anirban
 
Thanks,
>Shima
>
>
>
>
>________________________________
> From: Anirban <reach.anirban.ghosh at gmail.com>
>To: Shima Arasteh <shima_arasteh2001 at 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_arasteh2001 at 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.ghosh at gmail.com>
>>To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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_arasteh2001 at 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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