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[求助] editconf 和pdb2gmx坐标转换错误

各位MD大侠，
最近准备在gromacs中建聚合物的top文件，于是采用一个CF3CF2CF2CF3的结构按照在rtp文件中添加残基的方式建立力场，这一块倒是成功了，初始pdb坐标为：
HETATM 1  C1  PSFB    1    -5.110 2.179  -2.411                      C
HETATM 2  C2  PSFB    1    -3.581 2.024  -2.520                      C
HETATM 3  F11 PSFB    1    -5.771 0.846  -2.466                      F
HETATM 4  F12 PSFB    1    -5.595 3.012  -3.547                      F
HETATM 5  F13 PSFB    1    -5.463 2.856  -1.130                      F
HETATM 6  F21 PSFB    1    -2.964 3.378  -2.469                      F
HETATM 7  F22 PSFB    1    -3.253 1.384  -3.825                      F
HETATM 8  C1  PSFE    2    -3.033 1.154  -1.366                      C
HETATM 9  F11 PSFE    2    -3.627  -0.210  -1.445                      F
HETATM 10  F12 PSFE    2    -3.386 1.771  -0.058                      F
HETATM 11  C2  PSFE    2    -1.498 1.031  -1.450                      C
HETATM 12  F21 PSFE    2    -1.099 0.398  -2.737                      F
HETATM 13  F22 PSFE    2    -1.019 0.186  -0.321                      F
HETATM 14  F23 PSFE    2    -0.871 2.379  -1.344                      F
END
执行
editconf -f psf.pdb -o psf.gro
后得到的gro文件如下：
S  C  A  M  O  R  G
14
0PSFB C1 1  -0.511 0.000 0.900
0PSFB C2 2  -0.358 0.100 0.400
0PSFB F11 3  -0.577 0.100 0.600
0PSFB F12 4  -0.559 0.500 0.200
0PSFB F13 5  -0.546 0.300 0.600
0PSFB F21 6  -0.296 0.400 0.800
0PSFB F22 7  -0.325 0.300 0.400
0PSFE C1 8  -0.303 0.300 0.400
0PSFE F11 9  -0.362 0.700 0.000
0PSFE F12 10  -0.338 0.600 0.100
0PSFE C2 11  -0.149 0.800 0.100
0PSFE F21 12  -0.109 0.900 0.800
0PSFE F22 13  -0.101 0.900 0.600
0PSFE F23 14  -0.087 0.100 0.900
0.00000 0.00000 0.00000
~
可以看到pdb和gro文件中y和z坐标值完全不一致，现在也不知道错误出在哪里？
执行pdb2gmx的屏幕输出为
Reading test3.pdb...
WARNING: all CONECT records are ignored
Read 14 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 0 residues with 14 atoms

  chain  #res #atoms
  1 ' '    2    14

WARNING: there were 3 atoms with zero occupancy and 9 atoms with
      occupancy unequal to one (out of 14 atoms). Check your pdb file.

Opening force field file ./oplsaa_nafion.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa_nafion)
Opening force field file ./oplsaa_nafion.ff/aminoacids.rtp
Residue 64
Sorting it all out...
Opening force field file ./oplsaa_nafion.ff/aminoacids.hdb
Opening force field file ./oplsaa_nafion.ff/aminoacids.n.tdb
Opening force field file ./oplsaa_nafion.ff/aminoacids.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 (14 atoms, 2 residues)
Warning: Starting residue PSFB0 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue PSFE0 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms....
Now there are 2 residues with 14 atoms
Making bonds...
Warning: Long Bond (1-2 = 0.323042 nm)
Warning: Long Bond (1-3 = 0.861571 nm)
Warning: Long Bond (1-4 = 0.425705 nm)
Warning: Long Bond (1-5 = 0.532362 nm)
Warning: Long Bond (5-6 = 0.503829 nm)
Warning: Long Bond (8-9 = 0.568754 nm)
Warning: Long Bond (8-10 = 0.425705 nm)
Warning: Long Bond (8-11 = 0.603089 nm)
Warning: Long Bond (11-12 = 0.708237 nm)
Warning: Long Bond (11-13 = 0.512156 nm)
Warning: Long Bond (11-14 = 1.06482 nm)
Number of bonds was 14, now 13
Generating angles, dihedrals and pairs...
Before cleaning: 27 pairs
Before cleaning: 27 dihedrals
Keeping all generated dihedrals
Making cmap torsions...There are 27 dihedrals, 0 impropers, 24 angles
         27 pairs,    13 bonds and    0 virtual sites
Total mass 238.028 a.m.u.
Total charge -0.162 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.1#

Writing coordinate file...
            --------- PLEASE NOTE ------------
You have successfully generated a topology from: test3.pdb.
The Oplsaa_nafion force field is used.
            --------- ETON ESAELP ------------

gcq#121: "Step On the Brakes" (2 Unlimited)
附件上传建立聚合物力场的的一个初始步骤，也供初学者参考

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