[gmx-users] Missing Residues are list ind pdb file

[Jack Shultz]

I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the
non-standard residues. Re-named n-terminal and c-terminal residues. Took out
connects because that worked last time though I'm uncertain if connect
really maters.

Another issue with preping a protein. Its says I a missing H and HA for this
residue, but have those atoms listed there. Why does it say CYSH instead of
CYS2 on residue 15 ???
ffamber99sb.hdb does not list CYSH as a resdue.

http://boinc.drugdiscoveryathome.com/protein.pdb.txt
http://boinc.drugdiscoveryathome.com/pdb2gmx.txt


ATOM 232 N CYS2 15 5.467 7.021 7.435 1.00 0.00

ATOM 233 H CYS2 15 6.122 7.731 7.139 1.00 0.00

ATOM 234 CA CYS2 15 5.957 5.650 7.604 1.00 0.00

ATOM 235 HA CYS2 15 5.114 4.975 7.752 1.00 0.00

ATOM 236 CB CYS2 15 6.737 5.195 6.365 1.00 0.00

ATOM 237 2HB CYS2 15 6.774 4.106 6.322 1.00 0.00

ATOM 238 3HB CYS2 15 6.264 5.578 5.461 1.00 0.00

ATOM 239 SG CYS2 15 8.466 5.762 6.309 1.00 0.00

ATOM 240 HG CYS2 15 8.764 5.185 5.148 1.00 0.00

ATOM 241 C CYS2 15 6.841 5.543 8.845 1.00 0.00

ATOM 242 O CYS2 15 7.324 4.457 9.169 1.00 0.00

WARNING: atom H is missing in residue CYSH 15 in the pdb file
         You might need to add atom H to the hydrogen database of residue
CYSH
         in the file ff???.hdb (see the manual)


WARNING: atom HA is missing in residue CYSH 15 in the pdb file
         You might need to add atom HA to the hydrogen database of residue
CYSH
         in the file ff???.hdb (see the manual)


WARNING: atom HB1 is missing in residue CYSH 15 in the pdb file
         You might need to add atom HB1 to the hydrogen database of residue
CYSH
         in the file ff???.hdb (see the manual)


WARNING: atom HB2 is missing in residue CYSH 15 in the pdb file
         You might need to add atom HB2 to the hydrogen database of residue
CYSH
         in the file ff???.hdb (see the manual)


-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
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