RE： [gmx-users] A very strange problem about version of pdb2gmx
英雄不再寂寞
xiaowu759 at qq.com
Tue Oct 19 08:25:19 CEST 2010
Dear gmxers,
I have reinstalled the gmx-4.5.1 and this time the pdb2gmx is found to work using the same input and parameter files. So I consider that the "very strange" problem is due to some modified file which is unknown yet for me. Thanks again for your attention.
Sincerely, yours
Chaofu Wu, Dr.
------------------ 原始邮件 ------------------
发件人: "Justin A. Lemkul"<jalemkul at vt.edu>;
发送时间: 2010年10月17日(星期天) 晚上8:21
收件人: "Discussion list for GROMACS users"<gmx-users at gromacs.org>;
主题: Re: [gmx-users] A very strange problem about version of pdb2gmx
英雄不再寂寞 wrote:
> Dear gmxers,
> Yesterday, I posted a mail titled "pdb2gmx stop at "AtomType 1" "
> where I mentioned that I used gmx-4.5.1. The resulting problem is again
> posted below. Today, I turn to the gmx-4.0.7, and use the same pdb
> and rtp files with the name modified to compatible to the version.
> Strangely, it is found that the pdb2gmx of this version can generate the
> top file without any errors. Could you give me clues to why the latest
> version can not whereas the older version can? To get the clear help, my
> pdb and rtp files are also posted below. Thanks a lot for any reply.
Your system works for me under version 4.5.1, after fixing the naming mismatch
you have between your .pdb file ("MOL") and .rtp file ("DET"). I suppose your
actual input files have the correct names, though, otherwise this combination
would have generated a fatal error, not a hang.
-Justin
> Chaofu Wu, Dr.
>
> My command line and the screen output:
> xiaowu759 at linux-s38y:~/workshop
> <mailto:xiaowu759 at linux-s38y:~/workshop>> pdb2gmx -f deta.pdb -o
> deta.gro -p deta.top -i deta.itp -ter
> :-) G R O M A C S (-:
> Gromacs Runs One Microsecond At Cannonball Speeds
> :-) VERSION 4.5.1 (-:
> ......
> Opening force field file oplsaa.ff/aminoacids.r2b
> Reading deta.pdb...
> Read 20 atoms
> Analyzing pdb file
> Splitting PDB chains based on TER records or changing chain id.
> There are 1 chains and 0 blocks of water and 1 residues with 20 atoms
> chain #res #atoms
> 1 ' ' 1 20
> All occupancies are one
> Opening force field file oplsaa.ff/atomtypes.atp
> Atomtype 1
>
> My pdb file:
> ATOM 1 N1 MOL 1 -5.199 1.343 0.334 1.00
> 0.00 N
> ATOM 2 C2 MOL 1 -4.582 0.639 1.470 1.00
> 0.00 C
> ATOM 3 C3 MOL 1 -3.897 1.462 2.593 1.00
> 0.00 C
> ATOM 4 N4 MOL 1 -3.194 0.615 3.574 1.00
> 0.00 N
> ATOM 5 C5 MOL 1 -2.373 1.331 4.566 1.00
> 0.00 C
> ATOM 6 C6 MOL 1 -1.520 0.397 5.464 1.00
> 0.00 C
> ATOM 7 N7 MOL 1 -0.684 1.133 6.432 1.00
> 0.00 N
> ATOM 8 H12 MOL 1 -4.614 2.067 -0.035 1.00
> 0.00 H
> ATOM 9 H11 MOL 1 -6.128 1.694 0.483 1.00
> 0.00 H
> ATOM 10 H22 MOL 1 -3.826 -0.053 1.056 1.00
> 0.00 H
> ATOM 11 H21 MOL 1 -5.345 -0.016 1.926 1.00
> 0.00 H
> ATOM 12 H31 MOL 1 -4.628 2.144 3.065 1.00
> 0.00 H
> ATOM 13 H32 MOL 1 -3.141 2.116 2.124 1.00
> 0.00 H
> ATOM 14 H41 MOL 1 -3.854 0.018 4.043 1.00
> 0.00 H
> ATOM 15 H51 MOL 1 -2.980 2.003 5.204 1.00
> 0.00 H
> ATOM 16 H52 MOL 1 -1.679 1.992 4.016 1.00
> 0.00 H
> ATOM 17 H62 MOL 1 -0.857 -0.180 4.795 1.00
> 0.00 H
> ATOM 18 H61 MOL 1 -2.188 -0.346 5.939 1.00
> 0.00 H
> ATOM 19 H72 MOL 1 -0.023 0.541 6.916 1.00
> 0.00 H
> ATOM 20 H71 MOL 1 -1.253 1.554 7.143 1.00
> 0.00 H
> TER
> My rtp file:
> [ DET ]
> [ atoms ]
> N1 opls_900 -0.900 1
> H11 opls_909 0.360 1
> H12 opls_909 0.360 1
> C2 opls_906 0.060 1
> H21 opls_911 0.060 1
> H22 opls_911 0.060 1
> C3 opls_907 0.080 2
> H31 opls_911 0.060 2
> H32 opls_911 0.060 2
> N4 opls_901 -0.780 2
> H41 opls_910 0.380 2
> C5 opls_907 0.080 2
> H51 opls_911 0.060 2
> H52 opls_911 0.060 2
> C6 opls_906 0.060 3
> H61 opls_911 0.060 3
> H62 opls_911 0.060 3
> N7 opls_900 -0.900 3
> H71 opls_909 0.360 3
> H72 opls_909 0.360 3
> [ bonds ]
> N1 H11
> N1 H12
> N1 C2
> C2 H21
> C2 H22
> C2 C3
> C3 H31
> C3 H32
> C3 N4
> N4 H41
> N4 C5
> C5 H51
> C5 H52
> C5 C6
> C6 H61
> C6 H62
> C6 N7
> N7 H71
> N7 H72
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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