Re: [gmx-users] CHARMM27 hates my DMPC

[Justin Lemkul]

On 4/4/17 9:39 AM, Vytautas Rakeviius wrote:

Thanks, I reused DMPC layers from CHARMM-GUI after some editing.
I was able to pin-down issue here, test file:
http://www.mediafire.com/file/usuv55c3j505ec2/test.pdb
I can do: 
gmx pdb2gmx -f test.pdb -o test.gro -water spce

Without error. But if I do: 

gmx pdb2gmx -f test.pdb -o test.gro -water spce -ignh
I get error about hydrogen which I try to ignore. Very strange for me. -ignh
option is not possible with CHARMM ff?




Sure it is, but only when applied properly.

-ignh tells pdb2gmx to ignore H atoms and try to rebuild them.  If you haven't 
constructed a suitable .hdb entry for your residue, you're just going to cause 
errors for yourself because now you've ignored atoms, which are considered missing.


-Justin




On Tuesday, April 4, 2017 3:59 PM, Justin Lemkul  wrote:




On 4/4/17 8:52 AM, Vytautas Rakeviius wrote:

Hello,
I have my system with DMPC bilayers in pdb and try to convert it into GROMACS

input. Because system is with lipids I think chose CHARMM27 ff. But still I get
lots of warnings like that:


https://pastebin.com/K8dHKkUi
Also I add my DMPC pdb as example. What should I do? Rename all my DMPC

atoms?Thanks for all suggestions.






This is the same with any force field; the atom names have to match the force
field's expectations.

If you're just trying to build a DMPC bilayer, construct one using CHARMM-GUI.
It's guaranteed to have CHARMM-compliant nomenclature (and you should be using
CHARMM36 for lipids, anyway, because the CHARMM27 parameters are not nearly as
good for lipids).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu  |
(410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


==




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] CHARMM27 hates my DMPC

[Vytautas Rakeviius]

Thanks, I reused DMPC layers from CHARMM-GUI after some editing.I was able to 
pin-down issue here, test 
file:http://www.mediafire.com/file/usuv55c3j505ec2/test.pdbI can do:gmx pdb2gmx 
-f test.pdb -o test.gro -water spce
Without error. But if I do:gmx pdb2gmx -f test.pdb -o test.gro -water spce 
-ignhI get error about hydrogen which I try to ignore. Very strange for me. 
-ignh option is not possible with CHARMM ff?


 

On Tuesday, April 4, 2017 3:59 PM, Justin Lemkul  wrote:
 

 

On 4/4/17 8:52 AM, Vytautas Rakeviius wrote:
> Hello,
> I have my system with DMPC bilayers in pdb and try to convert it into GROMACS 
> input. Because system is with lipids I think chose CHARMM27 ff. But still I 
> get lots of warnings like that:
>
> https://pastebin.com/K8dHKkUi
> Also I add my DMPC pdb as example. What should I do? Rename all my DMPC 
> atoms?Thanks for all suggestions.
>
>

This is the same with any force field; the atom names have to match the force 
field's expectations.

If you're just trying to build a DMPC bilayer, construct one using CHARMM-GUI. 
It's guaranteed to have CHARMM-compliant nomenclature (and you should be using 
CHARMM36 for lipids, anyway, because the CHARMM27 parameters are not nearly as 
good for lipids).

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==


   
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Re: [gmx-users] CHARMM27 hates my DMPC

[Justin Lemkul]

On 4/4/17 8:52 AM, Vytautas Rakeviius wrote:

Hello,
I have my system with DMPC bilayers in pdb and try to convert it into GROMACS 
input. Because system is with lipids I think chose CHARMM27 ff. But still I get 
lots of warnings like that:

https://pastebin.com/K8dHKkUi
Also I add my DMPC pdb as example. What should I do? Rename all my DMPC 
atoms?Thanks for all suggestions.




This is the same with any force field; the atom names have to match the force 
field's expectations.


If you're just trying to build a DMPC bilayer, construct one using CHARMM-GUI. 
It's guaranteed to have CHARMM-compliant nomenclature (and you should be using 
CHARMM36 for lipids, anyway, because the CHARMM27 parameters are not nearly as 
good for lipids).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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[gmx-users] CHARMM27 hates my DMPC

[Vytautas Rakeviius]

Hello,
I have my system with DMPC bilayers in pdb and try to convert it into GROMACS 
input. Because system is with lipids I think chose CHARMM27 ff. But still I get 
lots of warnings like that: 

https://pastebin.com/K8dHKkUi
Also I add my DMPC pdb as example. What should I do? Rename all my DMPC 
atoms?Thanks for all suggestions.


-- 
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