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:
xiaowu...@linux-s38y:~/workshop
<mailto:xiaowu...@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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
