[gmx-users] non-symmetric matrix and too large first values / NMA

David van der Spoel spoel at xray.bmc.uu.se
Thu May 15 12:02:01 CEST 2003

On Thu, 2003-05-15 at 11:35, medeawan at sohu.com wrote:
> Thanks for your answer David:
> Maybe I should give more detail about my calculation. The protein structures are getting from PDB and the DNA structures are building by insightII. In order to do the EM, I add the DNA H database to ffG43b1.hdb, and edit the ffG43b1.rtp to let the nucleic acids join together.
> I can give the commands I use step by step:
> pdb2gmx -f 1iii.pdb -p 2iii.top -o 2iii.gro -i 2iii.itp -ignh
> grompp_d -f em -c 2iii -p 2iii -o in -po in
> mdrun_d -v -s in -o af -c af -e af -g af -nice 0
> grompp_d -v -t af.trr -f nm.mdp -c af.gro -p 2iii.top -o bn.tpr -po bn.mdp
> mdrun_d -v -s bn.tpr -g h.log -mtx h.mtx
> g_nmeig_d -f h.mtx -s bn.tpr -o v.xvg -v v.trr

> Thanks for any help.
>                                           Sincerely yours
>                                           Medeawan

Evrything looks fine as far as I can tell...

Maybe Bert can comment???

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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