On Mon, Oct 27, 2008 at 10:21 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>
> Peyman Yamin wrote:
>
>> On Monday 27 October 2008 15:07, Justin A. Lemkul wrote:
>>
>>> Peyman Yamin wrote:
>>>
On Monday 27 October 2008 14:03, Justin A. Lemkul wrote:
Actually I'm doing a funny mi
On Monday 27 October 2008 15:12, Justin A. Lemkul wrote:
> Peyman Yamin wrote:
> > On Monday 27 October 2008 14:08, Mark Abraham wrote:
> >> Peyman Yamin wrote:
> >>> Dear GMX users,
> >>>
> >>> I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the
> >>> structure with the Na replaced
Peyman Yamin wrote:
On Monday 27 October 2008 15:07, Justin A. Lemkul wrote:
Peyman Yamin wrote:
On Monday 27 October 2008 14:03, Justin A. Lemkul wrote:
Actually I'm doing a funny mistake telling I should replace an O with an
Na! (probably because of high adrenaline level in my blood for th
On Monday 27 October 2008 15:07, Justin A. Lemkul wrote:
> Peyman Yamin wrote:
> > On Monday 27 October 2008 14:03, Justin A. Lemkul wrote:
> >
> > Actually I'm doing a funny mistake telling I should replace an O with an
> > Na! (probably because of high adrenaline level in my blood for the
> > dea
Peyman Yamin wrote:
On Monday 27 October 2008 14:08, Mark Abraham wrote:
Peyman Yamin wrote:
Dear GMX users,
I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the
structure with the Na replaced with O.
That doesn't make sense to me.
I get a .top with this from prodrg and try
Peyman Yamin wrote:
On Monday 27 October 2008 14:03, Justin A. Lemkul wrote:
Actually I'm doing a funny mistake telling I should replace an O with an Na!
(probably because of high adrenaline level in my blood for the deadline is
near!) I should just put one Na beside the O I have! I simply h
On Monday 27 October 2008 14:03, Justin A. Lemkul wrote:
Actually I'm doing a funny mistake telling I should replace an O with an Na!
(probably because of high adrenaline level in my blood for the deadline is
near!) I should just put one Na beside the O I have! I simply have a PO4
where one O h
On Monday 27 October 2008 14:08, Mark Abraham wrote:
> Peyman Yamin wrote:
> > Dear GMX users,
> >
> > I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the
> > structure with the Na replaced with O.
>
> That doesn't make sense to me.
>
> > I get a .top with this from prodrg and try t
Thanks a lot for the replies,
I replace the O in DPPG because I thought it's practical to get the topology
of the quasi-DPPG (which has no charge cause the O is connected to the P)
from prodrg, and then delete the O and replace it with Na and delete the bond
of P with it and try to tell gromacs
Andreas
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On Behalf Of Peyman Yamin
> Sent: 27 October 2008 12:36
> To: gmx-users
> Subject: [gmx-users] Adding Na ions to DPPG
>
> Dear GMX users,
>
> I want to add sodium ions (Na+) t
Peyman Yamin wrote:
Dear GMX users,
I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure
with the Na replaced with O.
That doesn't make sense to me.
I get a .top with this from prodrg and try to
add the Na manually at the right place by removing the corresponding O
Peyman Yamin wrote:
Dear GMX users,
I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure
with the Na replaced with O. I get a .top with this from prodrg and try to
add the Na manually at the right place by removing the corresponding O. I use
GROMOS 96.1 forcefield.
Dear GMX users,
I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure
with the Na replaced with O. I get a .top with this from prodrg and try to
add the Na manually at the right place by removing the corresponding O. I use
GROMOS 96.1 forcefield. GMX version 3.3.1. I hav
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