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zxy964777869铜虫 (正式写手)
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[求助]
editconf 和pdb2gmx坐标转换错误
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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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2013-02-28 15:08:17, 14.79 K
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zxy964777869
铜虫 (正式写手)
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，发现为文件内部坐标位置的错误，在将pdb文件的第五列和第六列之间减少一个空格后，生成的gro文件就正常了，还是第一次遇到这种无厘头的错误。看来MS生成的pdb文件也应该小心 
2楼2013-03-01 13:48:12
zxy964777869
铜虫 (正式写手)
- 应助: 16 (小学生)
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- 性别: GG
- 专业: 理论和计算化学
3楼2013-03-01 13:59:59
