[gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 34
zhangzhengc at mail.iggcas.ac.cn
Mon Nov 9 07:55:34 CET 2015
I did some operations on my pdb or gro format file, for example, I deleted some atoms randomly to mimic a hole, then I had to re-number atoms in the pdb or gro format file by my code. The re-new pdb or gro file like picture 1 LINK: http://d.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=81b1352c18178a82ca3c7fa5c63802b0/cefc1e178a82b90149070cd3758da9773812efac.jpg?referer=54bbeb0fafec8a134d0d63d04962&x=.jpg,
thengromacs given errors like below picture 2 LINK: http://e.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=aec123e3ce95d143de76e42643cbf33f/d833c895d143ad4b3d75892084025aafa50f06f3.jpg?referer=c2157104b51c87018fa186d66292&x=.jpg,
but, I wrote itp and n2t file actually and there were no errors when uesd in others pdb or gro format structure file below 99999 atoms. I consulted pdb web, I found that pdb format file reset 100,000th atom`s number to zero, then I reset the 100,000th atom number to 0, it shows in below picture 3 LINK: http://h.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=2f6ce308ba3eb13540c7b7be9625d9ee/18d8bc3eb13533fa2ded5cceaed3fd1f40345bf3.jpg?referer=7d7df4241dd5ad6ef3ee50daa591&x=.jpg.
Gromacs given errors again when I run jobs showed in below picture 4 LINK: http://f.picphotos.baidu.com/album/s%3D550%3Bq%3D90%3Bc%3Dxiangce%2C100%2C100/sign=711787ced41b0ef468e8985bedff20e7/7c1ed21b0ef41bd578bb271457da81cb38db3d62.jpg?referer=ace4f085b519ebc4996f42a97b21&x=.jpg.
Thanks a lot.
> Message: 5
> Date: Sun, 08 Nov 2015 09:14:39 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] How to build a correct structure file beyond
> 99999 atoms using pdb or gro extend format ?
> <CAMNuMAS=_DcwbJeH1S9+z62kz9h6vhLmQ9yf1bu8JcZfk9hY8A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> What errors?
> On Sun, 8 Nov 2015 04:33 ??? <tianhuiquan0415 at 126.com> wrote:
> > Dear all,
> > I worte itp file and n2t file of myself, and went some runs, gromacs done
> > well when I built a pdb or gro extend format structure file contained less
> > than 99999 atoms, but gromacs will given errors when numbers of atoms are
> > beyond 99999 in above structure file. I consulted pdb web, and found that
> > pdb format file reset the 100,000th atom's number to 0, then I did same way
> > as pdb, but gromacs given errors again, how should I do to correct my
> > structure file?
> > Thanks in advance.
> > --
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> End of gromacs.org_gmx-users Digest, Vol 139, Issue 34
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