[gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 34

[Peter Stern]

Hi,



All your links give me the following, so I can't see what errors you are getting:
403 Forbidden
________________________________
JSP3/2.0.4



But, you don't have to renumber the atoms in your PDB file.  Gromacs ignores those numbers and uses its own numbers.  Otherwise, how could it deal with numbers over 99,999 which won't fit into the pdb file's I5 format for atom numbers?  And when pdb2gmx adds hydrogen atoms it obviously has to renumber the coordinates.  It is possible that by editing your pdb or gro files you are introducing errors, but I don't know.



Regards,

Peter Stern



-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of ???
Sent: Monday, November 09, 2015 8:55 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 34



Dear,

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<mailto:mark.j.abraham at gmail.com>>

> To: gmx-users at gromacs.org<mailto: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 ?

> Message-ID:

>  <CAMNuMAS=_DcwbJeH1S9+z62kz9h6vhLmQ9yf1bu8JcZfk9hY8A at mail.gmail.com<mailto:CAMNuMAS=_DcwbJeH1S9+z62kz9h6vhLmQ9yf1bu8JcZfk9hY8A at mail.gmail.com>>

> Content-Type: text/plain; charset=UTF-8

>

> Hi,

>

> What errors?

>

> Mark

>

> On Sun, 8 Nov 2015 04:33 ??? <tianhuiquan0415 at 126.com<mailto: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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