How to create protein XXX_nowat.pdb and correct gninatypes files

[gaoshan2006]

I am trying to re-create those pre-processed data. I am encountering 2 problems for creating protein's gninatypes files.
1) Remove water and hydrogen from XXX_protein.pdb to generate XXX_nowat.pdb. I only retain those lines beginning with "ATOM" except for hydrogen by my own code. However, sometimes my results are a bit different with XXX_nowat.pdb in the downloaded datasets. I notice some of the XXX_nowat.pdb in datasets cut the protein chains "B" compared with the original protein PDB file if the protein has more than 2 chains, but not always. Is there a script to create XXX_nowat.pdb to share with me ?

2）Create XXX_rec_0.gninatypes. Even though I am using the ready-made XXX_nowat.pdb file to create gninatypes files by "gninatyper". The files generated by my gninatyper are also different with the existing XXX_rec_0.gninatypes. I compared the 2 result files and find the atoms coordinate are actually right, but some atoms' types are different . E.g. the "NitrogenXSDonor" in the ready-made file is labeled as "NitrogenXSAcceptor" in my result, and "AromaticCarbonXSHydrophobe" is labeled as "AliphaticCarbonXSHydrophobe". Is it caused by my gnina version , "master:e60ccc0+", newer than the ready-made gninatypes files ?
Thanks a lot !

[gaoshan2006]

my_4c5d_rec_0_gninatypes.zip I attached my 4c5d protein gninatypes result and the ready-made file

[gaoshan2006]

The atom types differences between my gninatypes file (generated from 4c5d_nowat.pdb) with the ready-made 4c5d_rec_0. gninatypes file are partly listed as belows:

< my_4c5d_rec_0.gninatypes

4c5d_rec_0.gninatypes 76c76 < N NitrogenXSAcceptor 14.711000 -18.590000 -34.390999

N NitrogenXSDonor 14.711000 -18.590000 -34.390999 78c78 < N NitrogenXSDonor 16.169001 -18.809999 -36.169998

N NitrogenXSDonorAcceptor 16.169001 -18.809999 -36.169998 224,225c224,225 < C AliphaticCarbonXSHydrophobe 9.926000 -25.657000 -33.645000 < C AliphaticCarbonXSNonHydrophobe 10.115000 -24.997999 -32.470001

C AromaticCarbonXSHydrophobe 9.926000 -25.657000 -33.645000 C AromaticCarbonXSNonHydrophobe 10.115000 -24.997999 -32.470001 227c227 < N NitrogenXSAcceptor 11.182000 -24.132000 -32.577000

N NitrogenXSDonor 11.182000 -24.132000 -32.577000 311c311 < N NitrogenXSAcceptor -2.313000 -23.274000 -30.302000

N NitrogenXSDonor -2.313000 -23.274000 -30.302000 313c313 < N NitrogenXSDonor -2.653000 -22.570999 -32.479000

N NitrogenXSDonorAcceptor -2.653000 -22.570999 -32.479000 385c385 < N NitrogenXSAcceptor -17.170000 -36.254002 -21.774000

N NitrogenXSDonor -17.170000 -36.254002 -21.774000 387c387 < N NitrogenXSDonor -15.266000 -37.056000 -20.759001

N NitrogenXSDonorAcceptor -15.266000 -37.056000 -20.759001 408c408 < N NitrogenXSAcceptor -23.131001 -29.589001 -26.837999

N NitrogenXSDonor -23.131001 -29.589001 -26.837999 411c411 < N NitrogenXSDonor -24.007999 -31.716000 -26.934999

N NitrogenXSDonorAcceptor -24.007999 -31.716000 -26.934999 419c419 < N NitrogenXSAcceptor -26.429001 -29.354000 -21.033001

N NitrogenXSDonor -26.429001 -29.354000 -21.033001 422c422 < N NitrogenXSDonor -26.714001 -31.531000 -20.351000

N NitrogenXSDonorAcceptor -26.714001 -31.531000 -20.351000 496,499c496,499 < C AliphaticCarbonXSNonHydrophobe -18.302000 -13.891000 -9.014000 < N NitrogenXSAcceptor -19.482000 -13.221000 -8.785000 < C AliphaticCarbonXSNonHydrophobe -18.535999 -15.188000 -8.701000 < C AliphaticCarbonXSNonHydrophobe -20.389000 -14.074000 -8.339000

C AromaticCarbonXSNonHydrophobe -18.302000 -13.891000 -9.014000 N NitrogenXSDonor -19.482000 -13.221000 -8.785000 C AromaticCarbonXSNonHydrophobe -18.535999 -15.188000 -8.701000 C AromaticCarbonXSNonHydrophobe -20.389000 -14.074000 -8.339000 .............. Here are the two types files 4c5d_types_diff.zip

[dkoes]

Different versions of openbabel will generate different protonation states.