Problem with whitespace in PQR file

[sobolevnrm]

          Hi! The issue with such naming scheme for protonated ASP and GLU remains...

And there is another one, which is naming atoms directly involved in a dissulfide bond as part of a "DISU" residue name

Used the command
$ pdb2pqr protein.pdb protonated.pqr --ff CHARMM --ffout=CHARMM --titration-state-method=propka --with-ph=4 -o 4

The cysteine residues below (numbers 48 and 89 of PDB ID - chain A of 3bpm) are involved in a dissulfide bond of a cysteine protease protein. When preparing this system to run molecular dynamics simulations it raises an error since there are atoms from the same chain and residue numbering with different names (CYS and DISU).
Moreover, there is no space between atom names 1CB and 1SG to "DISU"; It should only be "CB CYS" and "SG CYS". The absence of space between atom names and residue name is also part of protonated GLU and ASP

ATOM 1024 N GLU 67 14.715 0.462 -3.470 -0.4700 1.8500
ATOM 1025 CA GLU 67 14.634 -0.356 -2.275 0.0700 2.2750
ATOM 1026 CB GLU 67 13.681 -1.585 -2.414 -0.1800 2.1750
ATOM 1027 CG GLUP 67 12.188 -1.077 -2.494 -0.2100 2.1750
ATOM 1028 CD GLUP 67 11.677 -1.084 -3.947 0.7500 2.0000
ATOM 1029 OE1GLUP 67 10.500 -1.169 -4.271 -0.5500 1.7000
ATOM 1030 OE2GLUP 67 12.716 -1.214 -4.865 -0.6100 1.7700
ATOM 1031 C GLU 67 15.968 -0.840 -1.728 0.5100 2.0000
ATOM 1032 O GLU 67 16.118 -0.876 -0.548 -0.5100 1.7000
ATOM 1033 HN GLU 67 14.298 0.110 -4.407 0.3100 0.2245
ATOM 1034 HA GLU 67 14.142 0.166 -1.540 0.0900 1.3200
ATOM 1035 HB2 GLU 67 13.872 -2.017 -3.245 0.0900 1.3200
ATOM 1036 HB1 GLU 67 13.754 -2.110 -1.619 0.0900 1.3200
ATOM 1037 HG2GLUP 67 11.647 -1.695 -1.982 0.0900 1.3200
ATOM 1038 HG1 GLU 67 12.177 -0.163 -2.176 0.0900 1.3200
ATOM 1039 HE2GLUP 67 12.422 -1.224 -5.753 0.4400 0.2245

ATOM 1113 N ASP 72 19.688 -0.513 2.566 -0.4700 1.8500
ATOM 1114 CA ASP 72 21.133 -0.205 2.918 0.0700 2.2750
ATOM 1115 CB ASPP 72 21.994 0.117 1.627 -0.2100 2.1750
ATOM 1116 CG ASPP 72 22.213 -1.046 0.639 0.7500 2.0000
ATOM 1117 OD1ASPP 72 22.132 -2.242 0.875 -0.5500 1.7000
ATOM 1118 OD2ASPP 72 22.509 -0.572 -0.684 -0.6100 1.7700
ATOM 1119 C ASP 72 21.309 0.777 4.014 0.5100 2.0000
ATOM 1120 O ASP 72 22.245 0.697 4.829 -0.5100 1.7000
ATOM 1121 HN ASP 72 19.360 -0.331 1.543 0.3100 0.2245
ATOM 1122 HA ASP 72 21.527 -1.099 3.211 0.0900 1.3200
ATOM 1123 HB2ASPP 72 21.527 0.863 1.148 0.0900 1.3200
ATOM 1124 HB1 ASP 72 22.886 0.440 1.948 0.0900 1.3200
ATOM 1125 HD2ASPP 72 22.531 0.386 -0.696 0.4400 0.2245

ATOM 616 N CYS A 41 16.020 -10.822 -0.571 -0.4700 1.8500
ATOM 617 CA CYS A 41 15.487 -10.991 0.754 0.0700 2.2750
ATOM 618 1CBDISU A 41 16.577 -10.699 1.769 -0.1000 2.1750
ATOM 619 1SGDISU A 41 17.237 -9.050 2.103 -0.0800 1.9750
ATOM 620 C CYS A 41 14.396 -9.913 0.935 0.5100 2.0000
ATOM 621 O CYS A 41 14.466 -8.888 0.309 -0.5100 1.7000
ATOM 622 HN CYS A 41 15.952 -9.915 -0.978 0.3100 0.2245
ATOM 623 HA CYS A 41 15.015 -11.957 0.861 0.0900 1.3200
ATOM 624 HB2 CYS A 41 17.415 -11.323 1.389 0.0900 1.3200
ATOM 625 HB1 CYS A 41 16.266 -11.201 2.710 0.0900 1.3200

ATOM 1206 N CYS 82 16.175 -9.286 6.418 -0.4700 1.8500
ATOM 1207 CA CYS 82 14.986 -10.007 5.938 0.0700 2.2750
ATOM 1208 1CBDISU 82 15.263 -11.312 5.189 -0.1000 2.1750
ATOM 1209 1SGDISU 82 16.357 -11.098 3.616 -0.0800 1.9750
ATOM 1210 C CYS 82 13.995 -10.374 7.086 0.5100 2.0000
ATOM 1211 O CYS 82 13.289 -11.310 6.984 -0.5100 1.7000
ATOM 1212 HN CYS 82 17.076 -9.760 6.651 0.3100 0.2245
ATOM 1213 HA CYS 82 14.490 -9.410 5.293 0.0900 1.3200
ATOM 1214 HB2 CYS 82 15.757 -11.937 5.769 0.0900 1.3200
ATOM 1215 HB1 CYS 82 14.416 -11.704 4.868 0.0900 1.3200

I've decided to use the amber naming scheme and later assigning in charmm-gui server, however I wish to prepare my system's locally. Is there any way to correct that?

Many thanks,
Mariana

Originally posted by @marianasimoesf in #358 (comment)

[sobolevnrm]

@marianasimoesf have you tried the pdb2pqr --whitespace option?

[marianasimoesf]

Yes, to add a space separating columns.
The thing is that if the residues were to be named correctly in a dissulfide bond, for example, we shouldn't have to use this other flag. I was aiming to add some more context to the problems such naming scheme may give to users