kehan777 commented 1 year ago

老师您好，谢谢您开发了这个软件。

我采用以下命令时，有数据产生（如图），但报错1a2k_min.pdb 不出现；

python BindPPI_AvgEns.py -i 1a2k mkdir: cannot create directory ‘/home/adsb/bindppi/bindppii/1a2k_out’: File exists At line 1451 of file /home/adsb/bindppi/charmm/build/cmake/cvio.F90 (unit = 35, file = 'fort.35') Fortran runtime error: End of file

Error termination. Backtrace:

0 0x7fce6f43c960 in ???

1 0x7fce6f43d4d9 in ???

2 0x7fce6f43e10f in ???

3 0x7fce6f69117b in ???

4 0x7fce6f691bdf in ???

5 0x7fce6f691cb4 in ???

6 0x7fce6f69406a in ???

7 0x7fce6f694947 in ???

8 0x564b98978214 in ???

9 0x564b9897d49f in ???

10 0x564b98c60bac in ???

11 0x564b9893321a in ???

12 0x564b9892febe in ???

13 0x7fce6ef07d8f in ???

14 0x7fce6ef07e3f in ???

15 0x564b9892ff14 in ???

16 0xffffffffffffffff in ???

Traceback (most recent call last): File "BindPPI_AvgEns.py", line 775, in min_add_chain() File "BindPPI_AvgEns.py", line 352, in min_add_chain f = open(pathoutput+'/'+pdb_low+'_min.pdb','r') FileNotFoundError: [Errno 2] No such file or directory: '/home/adsb/bindppi/bindppii/1a2k_out/1a2k_min.pdb'

是否以下代码，导致无法输出 1a2k_min.pdb, def frames(): pdball = [] pdb_low = pdb.lower() startframe = 100 if pdblow not in pdball: os.system('%s <%s/frame.inp path=%s protname=%s startframe=%s pathinput=%s> %s/frame%s.out' % (pathcharmm, pathinput, pathoutput, pdb_low, startframe, pathinput, pathoutput, pdb_low)) pdball.append(pdb_low)

文件 frame_1a2k.out 的部分内容如下：请问有什么办法解决吗？ CHARMM> read psf card name @path/@protname_charmm.psf Parameter: PATH -> "/HOME/ADSB/BINDPPI/BINDPPII/1A2K_OUT" Parameter: PROTNAME -> "1A2K" VOPEN> Attempting to open::/home/adsb/bindppi/bindppii/1a2k_out/1a2k_charmm.psf:: MAINIO> Protein structure file being read from unit 90. TITLE> PSF TITLE> DATE: 11/ 8/23 22:49:24 CREATED BY USER: adsb TITLE> * PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 444 Number of atoms = 7103 Number of groups = 2169 Number of bonds = 7195 Number of angles = 13004 Number of dihedrals = 19087 Number of impropers = 1279 Number of cross-terms = 438 Number of autogens = 0 Number of HB acceptors = 663 Number of HB donors = 778 Number of NB exclusions = 0 Total charge = -4.00000 VCLOSE: Closing unit 90 with status "KEEP"

CHARMM> read coor card name @path/@protname_charmm.crd Parameter: PATH -> "/HOME/ADSB/BINDPPI/BINDPPII/1A2K_OUT" Parameter: PROTNAME -> "1A2K" VOPEN> Attempting to open::/home/adsb/bindppi/bindppii/1a2k_out/1a2k_charmm.crd:: SPATIAL COORDINATES BEING READ FROM UNIT 90 TITLE> COORDS TITLE> DATE: 11/ 8/23 22:49:24 CREATED BY USER: ADSB TITLE> * VCLOSE: Closing unit 90 with status "KEEP"

CHARMM>

CHARMM> !!!!!!!!!!!!!! analysis of trajectory !!!!!!!!!!!!!!!!! CHARMM>

CHARMM> OPEN READ UNIT 35 FILE NAME @path/@protname_min.dcd Parameter: PATH -> "/HOME/ADSB/BINDPPI/BINDPPII/1A2K_OUT" Parameter: PROTNAME -> "1A2K" VOPEN> Attempting to open::/home/adsb/bindppi/bindppii/1a2k_out/1a2k_min.dcd:: OPNLGU> Unit 35 cannot be opened as /HOME/ADSB/BINDPPI/BINDPPII/1A2K_OUT/1A2K_MIN.DCD

  ***** LEVEL  0 WARNING FROM <OPNLGU> *****
  ***** "OPEN" not possible.

或者您能分享一下文件夹1a2k_out 输出结果的内容吗？放置github BindPPI 的文件夹下，谢谢您~

ZhengFF123 commented 12 months ago

Hi there,

Thank you for your report. We have uploaded the intermediate process output folder '1a2k_out' in an effort to assist you in resolving this issue. Please feel free to take a look and let us know if you need any further information or if there's anything else we can do to help.

Best regards

kehan777 commented 12 months ago

谢谢您分享了文件；我借用您提供的文件，运行之后，有新的问题向您请教~ Q1: charmm 无法生成xxx_min.pdb文件，查看 frame_1a2k.out 文件， CHARMM> OPEN READ UNIT 35 FILE NAME @path/@protname_min.dcd Parameter: PATH -> "/HOME/ADSB/BINDPPI/BINDPPII/1A2K_OUT" Parameter: PROTNAME -> "1A2K" VOPEN> Attempting to open::/home/adsb/bindppi/bindppii/1a2k_out/1a2k_min.dcd:: OPNLGU> Unit 35 cannot be opened as /HOME/ADSB/BINDPPI/BINDPPII/1A2K_OUT/1A2K_MIN.DCD

您提供的文件结果： CHARMM> OPEN READ UNIT 35 FILE NAME @path/@protname_min.dcd Parameter: PATH -> "/DATA/JIANG/AFFI/BINDPPI/1A2K_OUT" Parameter: PROTNAME -> "1A2K" VOPEN> Attempting to open::/data/jiang/affi/bindppi/1a2k_out/1a2k_min.dcd:: OPNLGU> Unit 35 opened for READONLY access to /data/jiang/affi/bindppi/1a2k_out/1a2k_min.dcd

CHARMM> TRAJECTORY FIRSTU 35 NUNIT 1 BEGIN @startframe Parameter: STARTFRAME -> "100" TRAJ: INITIATING READ OF A TRAJECTORY, OPTIONS; FIRSTU = 35 NUNIT = 1 SKIP = 1 这一步导致了后续xxx.min.pdb 无法生成；不知道是否为版本问题，我用 charmm 48b1，您的是 charmm(CHARMM) - Free Version 41b2 能否分享到网盘，我试一下安装

Q2: xxx__min.pdb 被mkdssp 读取，格式报错 /usr/bin/mkdssp -i /home/adsb/bindppi/bindppii/1a2k_out/1A2K_min.pdb -o /home/adsb/bindppi/bindppii/1a2k_out/1A2K_min.dssp Error parsing PDB at line 1 Error trying to load file "/home/adsb/bindppi/bindppii/1a2k_out/1A2K_min.pdb" Expected record CRYST1 but found ATOM

A2: 用dssp 4.x 会出现这个问题，已用dssp 3.x 解决 https://github.com/cmbi/dssp/releases

Q3: run_provean, 报错如下， BLAST Database error: No alias or index file found for protein database [/home/adsb/bindppi/Blastdb/] in search path [/home/adsb/bindppi/bindppii/1a2k_out::] psiblast failed (exit:512) 应下载 https://ftp.ncbi.nlm.nih.gov/blast/db/ 蛋白数据库的哪些内容？ nr.xxx.tar.gz 约206GB都要下载吗？