Hi, dear folks,
In CPHMD structure file, we change HSD to HSP in order to titrate this kind of residue. I have run the test case as kindly provided by you, it is fine. But, when it comes to my case which has a lot of histidine residues, in the output structure files some of the his residues have the name of HSD instead of HSP(but it still has two titratable hydrogens). I did change HSD to HSP and no structure file(psf,crd, pdb) contains HSD word any more. This really bothers me a lot. Look forward to your reply.
There is one thing that is not clear in your question. What are the "structure files" that you have problem with? Are they the "final.pdb" files under each "aa#" directory, or the bundle pdb file you generated using MMTSB toolset? Besides, could you post the "init.pdb" as well as some of the files that went wrong? It is much better if I can see where the problems happen.
Steven W.
What I mean is the initial strucutre files don't contain HSD word, but the output final.pdb files do.
Init.pdb
ATOM 128 N TYR 17 114.587 -36.951-183.614 1.00 2.03 PROAATOM 129 HN TYR 17 113.705 -36.834-183.154 1.00 0.00 PROAATOM 130 CA TYR 17 115.442 -37.993-183.092 1.00 2.86 PROAATOM 131 HA TYR 17 116.099 -38.327-183.884 1.00 0.00 PROAATOM 132 CB TYR 17 116.330 -37.475-181.923 1.00 2.67 PROAATOM 133 HB1 TYR 17 116.980 -36.662-182.311 1.00 0.00 PROAATOM 134 HB2 TYR 17 116.991 -38.286-181.556 1.00 0.00 PROAATOM 135 CG TYR 17 115.558 -36.914-180.751 1.00 2.46 PROAATOM 136 CD1 TYR 17 115.302 -37.713-179.625 1.00 2.00 PROAATOM 137 HD1 TYR 17 115.628 -38.742-179.614 1.00 0.00 PROAATOM 138 CE1 TYR 17 114.644 -37.183-178.506 1.00 2.00 PROAATOM 139 HE1 TYR 17 114.469 -37.809-177.641 1.00 0.00 PROAATOM 140 CZ TYR 17 114.245 -35.842-178.495 1.00 2.00 PROAATOM 141 OH TYR 17 113.643 -35.291-177.344 1.00 1.85 PROAATOM 142 HH TYR 17 113.492 -36.024-176.718 1.00 0.00 PROAATOM 143 CD2 TYR 17 115.138 -35.571-180.736 1.00 2.00 PROAATOM 144 HD2 TYR 17 115.335 -34.937-181.588 1.00 0.00 PROAATOM 145 CE2 TYR 17 114.486 -35.038-179.614 1.00 2.00 PROAATOM 146 HE2 TYR 17 114.185 -34.002-179.603 1.00 0.00 PROAATOM 147 C TYR 17 114.635 -39.219-182.695 1.00 2.04 PROAATOM 148 O TYR 17 113.435 -39.152-182.445 1.00 1.52 PROAATOM 149 N HSP 18 115.294 -40.393-182.699 1.00 2.03 PROAATOM 150 HN HSP 18 116.265 -40.374-182.960 1.00 0.00 PROAATOM 151 CA HSP 18 114.765 -41.699-182.326 1.00 2.86 PROAATOM 152 HA HSP 18 114.015 -41.949-183.065 1.00 0.00 PROAATOM 153 CB HSP 18 115.907 -42.748-182.407 1.00 2.67 PROAATOM 154 HB1 HSP 18 116.722 -42.441-181.715 1.00 0.00 PROAATOM 155 HB2 HSP 18 116.323 -42.726-183.438 1.00 0.00 PROAATOM 156 CD2 HSP 18 116.085 -45.014-181.164 1.00 1.98 PROAATOM 157 HD2 HSP 18 116.863 -44.830-180.429 1.00 0.00 PROAATOM 158 CG HSP 18 115.564 -44.183-182.098 1.00 2.46 PROAATOM 159 NE2 HSP 18 115.485 -46.230-181.337 1.00 1.90 PROAATOM 160 HE2 HSP 18 115.746 -47.086-180.857 1.00 0.00 PROAATOM 161 ND1 HSP 18 114.657 -44.912-182.817 1.00 1.90 PROAATOM 162 HD1 HSP 18 114.085 -44.608-183.600 1.00 0.00 PROAATOM 163 CE1 HSP 18 114.626 -46.147-182.337 1.00 1.98 PROAATOM 164 HE1 HSP 18 113.988 -46.952-182.685 1.00 0.00 PROAATOM 165 C HSP 18 114.079 -41.808-180.964 1.00 2.04 PROAATOM 166 O HSP 18 114.435 -41.135-179.999 1.00 1.52 PROA
final.pdb
ATOM 128 N TYR 17 113.627 -36.622-183.325 1.00 2.03 PROAATOM 129 HN TYR 17 112.690 -36.615-182.983 1.00 0.00 PROAATOM 130 CA TYR 17 114.407 -37.663-182.846 1.00 2.86 PROAATOM 131 HA TYR 17 114.997 -38.069-183.655 1.00 0.00 PROAATOM 132 CB TYR 17 115.399 -37.193-181.645 1.00 2.67 PROAATOM 133 HB1 TYR 17 115.972 -36.367-182.119 1.00 0.00 PROAATOM 134 HB2 TYR 17 116.156 -37.952-181.351 1.00 0.00 PROAATOM 135 CG TYR 17 114.651 -36.813-180.302 1.00 2.46 PROAATOM 136 CD1 TYR 17 114.327 -37.681-179.266 1.00 2.00 PROAATOM 137 HD1 TYR 17 114.631 -38.717-179.300 1.00 0.00 PROAATOM 138 CE1 TYR 17 113.758 -37.207-178.048 1.00 2.00 PROAATOM 139 HE1 TYR 17 113.476 -37.838-177.218 1.00 0.00 PROAATOM 140 CZ TYR 17 113.534 -35.842-177.935 1.00 2.00 PROAATOM 141 OH TYR 17 112.955 -35.318-176.763 1.00 1.85 PROAATOM 142 HH TYR 17 112.241 -35.871-176.437 1.00 0.00 PROAATOM 143 CD2 TYR 17 114.383 -35.388-180.103 1.00 2.00 PROAATOM 144 HD2 TYR 17 114.626 -34.686-180.888 1.00 0.00 PROAATOM 145 CE2 TYR 17 113.783 -34.982-178.925 1.00 2.00 PROAATOM 146 HE2 TYR 17 113.648 -33.931-178.718 1.00 0.00 PROAATOM 147 C TYR 17 113.410 -38.749-182.325 1.00 2.04 PROAATOM 148 O TYR 17 112.190 -38.553-182.334 1.00 1.52 PROAATOM 149 N HSD 18 113.969 -39.950-182.100 1.00 2.03 PROAATOM 150 HN HSD 18 114.958 -40.074-182.095 1.00 0.00 PROAATOM 151 CA HSD 18 113.211 -41.137-181.772 1.00 2.86 PROAATOM 152 HA HSD 18 112.154 -40.915-181.762 1.00 0.00 PROAATOM 153 CB HSD 18 113.528 -42.332-182.746 1.00 2.67 PROAATOM 154 HB1 HSD 18 114.619 -42.539-182.789 1.00 0.00 PROAATOM 155 HB2 HSD 18 113.280 -42.103-183.804 1.00 0.00 PROAATOM 156 CD2 HSD 18 113.453 -44.876-182.217 1.00 1.98 PROAATOM 157 HD2 HSD 18 114.499 -45.154-182.258 1.00 0.00 PROAATOM 158 CG HSD 18 112.903 -43.657-182.504 1.00 2.46 PROAATOM 159 NE2 HSD 18 112.412 -45.742-182.039 1.00 1.90 PROAATOM 160 HE2 HSD 18 112.477 -46.709-181.789 1.00 0.00 PROAATOM 161 ND1 HSD 18 111.569 -43.875-182.484 1.00 1.90 PROAATOM 162 HD1 HSD 18 110.977 -43.186-182.903 1.00 0.00 PROAATOM 163 CE1 HSD 18 111.264 -45.152-182.247 1.00 1.98 PROAATOM 164 HE1 HSD 18 110.284 -45.581-182.250 1.00 0.00 PROAATOM 165 C HSD 18 113.547 -41.659-180.379 1.00 2.04 PROAATOM 166 O HSD 18 114.724 -41.675-179.966 1.00 1.52 PROA
The problem most likely lies in MMTSB, not in CHARMM. If you check the residue names of histidine residues in the "final.crd" file (generated by CHARMM), these names should be correct. Since the dynamics is implemented using CHARMM, your titration simulations should not be affected. Thus I would suggest that you just ignore the "final.pdb" files and analyze your results using "init.pdb" and the trajectory files.
Steven
Thank you so much! I will check it.