From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Thu Dec 01 2016 - 00:27:37 CST
Hi Norman Geist,
Thank you for the suggestions and I have modified
the gromacs topology file by looking at the namd source code
"GromacsTopFile.C". It is working.
Thanks,
Subbarao Kanchi.
On Wed, Nov 30, 2016 at 2:15 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Have you tried sending your topology through one of the gromacs tools to
> check it is correct? Otherwise, since gromacs support in namd is rather
> rudimentary, you could also try to convert your gromacs files to amber
> format using the Parmed tool, either directly downloaded from github or
> shipped with the Ambertools 16, as:
>
>
>
> parmed
>
> parmed> gromber your.top your.gro
>
> parmed> outparm your.prmtop your.rst7
>
>
>
> It might also output errors your topology has issues. Later in namd you do;
>
>
>
> amber on
>
> parmfile your.prmtop
>
> ambercoor your.rst7
>
>
>
> Best wishes
>
>
>
> Norman Geist
>
>
>
> *Von:* Subbarao Kanchi [mailto:ksubbu85_at_gmail.com]
> *Gesendet:* Dienstag, 29. November 2016 11:25
> *An:* Norman Geist <norman.geist_at_uni-greifswald.de>
> *Cc:* namd-l_at_ks.uiuc.edu
> *Betreff:* Re: namd-l: Running gromacs in namd
>
>
>
> 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.
>
>
>
>
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:50 CST