Re: Running gromacs in namd

From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Tue Nov 29 2016 - 04:25:06 CST

Hi Norman Geist,
                        I have copied the *.itp into the topologies file
(.top) and end up with another error "Syntax error in ATOMS" as reported in
mailing list
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2003-2004/1102.html.
I do not find any solution to overcome the error.

Thanks
Subbarao Kanchi

On Tue, Nov 29, 2016 at 1:06 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> Well, the exact error is just:
>
>
>
> Molecule DMPC undefined
>
>
>
> This is because namd doesn’t follow linked *.itp files from your topology
> file. Please just copy the content of all required *.itp files into your
> *.top file and try again.
>
>
>
> Best of luck
>
>
>
> Norman Geist
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Subbarao Kanchi
> *Gesendet:* Dienstag, 29. November 2016 07:31
> *An:* mmakowsk_at_uci.edu
> *Cc:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: Running gromacs in namd
>
>
>
> Dear Michael Makowski,
>
> I am trying to run gromacs simulation
> in namd and getting the error "USING ARITHMETIC MEAN TO COMBINE L-J SIGMA
> PARAMETERS Molecule DMPC undefined" I have seen your post in the mailing
> list "http://www.ks.uiuc.edu/Research/namd/mailing_list/
> namd-l.2014-2015/1129.html". Could you let me know that how did you
> overcome this problem to run gromacs simulation in namd.
>
> Thanks,
>
> Subbarao Kanchi.
>
>
>

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