[gmx-users] long-bond warning during running
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Jul 3 15:29:20 CEST 2009
nitu sharma wrote:
> Dear all
You've broken something badly, like put the PDB information in columns
of the wrong width.
Mark
> I am doing simulation of Dna-protein complex with using amber
> tools with gromacs -4.0.3 . For this a/c to ffamber99.rtp file I have
> made lot of changes in .pdb file after that "pdb2gmx " starts working
> but it give to many warnings. like-
> Warning: Long Bond (291-293 = 0.86645 nm)
> Warning: Long Bond (291-310 = 1.08462 nm)
> Warning: Long Bond (293-294 = 0.429679 nm)
> Warning: Long Bond (293-307 = 0.767604 nm)
> Warning: Long Bond (294-296 = 0.443442 nm)
> Warning: Long Bond (297-298 = 0.737835 nm)
> Warning: Long Bond (297-307 = 0.595315 nm)
> Warning: Long Bond (298-299 = 0.808366 nm)
> Warning: Long Bond (298-300 = 0.707622 nm)
> Warning: Long Bond (300-302 = 0.738664 nm)
> Warning: Long Bond (302-303 = 0.860242 nm)
> Warning: Long Bond (302-306 = 0.427252 nm)
> Warning: Long Bond (306-307 = 0.60875 nm)
> Warning: Long Bond (308-310 = 0.931786 nm)
> Warning: Long Bond (308-313 = 0.828688 nm)
> Warning: Long Bond (280-281 = 0.417096 nm)
> Warning: Long Bond (314-315 = 0.265962 nm)
> Warning: Long Bond (314-316 = 0.501846 nm)
> Warning: Long Bond (314-317 = 0.407156 nm)
> Warning: Long Bond (317-318 = 0.316267 nm)
> Warning: Long Bond (321-323 = 0.735348 nm)
> Warning: Long Bond (321-336 = 0.672012 nm)
> Warning: Long Bond (323-324 = 0.634508 nm)
> Warning: Long Bond (326-327 = 0.510123 nm)
> Warning: Long Bond (326-334 = 0.951643 nm)
> Warning: Long Bond (327-329 = 0.510298 nm)
> Warning: Long Bond (329-330 = 0.433539 nm)
> Warning: Long Bond (330-331 = 0.458922 nm)
> Warning: Long Bond (332-334 = 0.592297 nm)
> Warning: Long Bond (334-335 = 0.412661 nm)
> Warning: Long Bond (336-338 = 0.907703 nm)
> Warning: Long Bond (336-341 = 0.905717 nm)
> Warning: Long Bond (313-314 = 0.702567 nm)
> Warning: Long Bond (342-343 = 0.704904 nm)
> Warning: Long Bond (342-344 = 0.808923 nm)
> Warning: Long Bond (342-345 = 0.860233 nm)
> Warning: Long Bond (349-369 = 0.402523 nm)
> Warning: Long Bond (351-352 = 0.825131 nm)
> Warning: Long Bond (352-354 = 0.708667 nm)
> Warning: Long Bond (352-371 = 0.772094 nm)
> Warning: Long Bond (354-355 = 0.431195 nm)
> Warning: Long Bond (354-368 = 0.342288 nm)
> Warning: Long Bond (355-357 = 0.514821 nm)
> Warning: Long Bond (357-358 = 0.517131 nm)
> Warning: Long Bond (359-360 = 0.640538 nm)
> Warning: Long Bond (359-361 = 0.511957 nm)
> Warning: Long Bond (361-363 = 0.632475 nm)
> Warning: Long Bond (363-364 = 0.252832 nm)
> Warning: Long Bond (363-367 = 0.550244 nm)
> Warning: Long Bond (367-368 = 0.593196 nm)
> Warning: Long Bond (369-371 = 0.415453 nm)
> Warning: Long Bond (369-374 = 0.611634 nm)
> Warning: Long Bond (341-342 = 0.830307 nm)
> Warning: Long Bond (375-378 = 0.422488 nm)
> Warning: Long Bond (378-379 = 0.251446 nm)
> Warning: Short Bond (382-384 = 0.034 nm)
> Warning: Long Bond (382-397 = 0.360644 nm)
> Warning: Long Bond (384-385 = 0.448028 nm)
> Warning: Long Bond (385-387 = 0.854859 nm)
> Warning: Long Bond (385-399 = 0.898552 nm)
> Warning: Long Bond (387-388 = 0.341151 nm)
> Warning: Long Bond (387-395 = 0.64161 nm)
> Warning: Long Bond (388-390 = 0.583816 nm)
> Warning: Long Bond (390-391 = 0.460305 nm)
> Warning: Long Bond (391-393 = 0.596343 nm)
> Warning: Long Bond (393-395 = 0.510843 nm)
> Warning: Long Bond (395-396 = 0.378148 nm)
> Warning: Long Bond (397-399 = 0.922111 nm)
> Warning: Long Bond (397-402 = 0.596553 nm)
> Warning: Long Bond (374-375 = 0.40299 nm)
> Warning: Long Bond (403-404 = 0.637247 nm)
> Warning: Long Bond (404-407 = 0.318624 nm)
> Warning: Long Bond (407-409 = 0.379685 nm)
> Warning: Long Bond (407-426 = 0.543994 nm)
> Warning: Long Bond (409-410 = 0.500324 nm)
> Warning: Long Bond (410-428 = 0.609291 nm)
> Warning: Long Bond (412-425 = 0.788185 nm)
> Warning: Long Bond (413-415 = 0.791283 nm)
> Warning: Long Bond (415-416 = 0.708127 nm)
> Warning: Long Bond (416-417 = 0.255204 nm)
> Warning: Long Bond (416-425 = 0.715307 nm)
> Warning: Long Bond (417-418 = 0.618501 nm)
> Warning: Long Bond (417-421 = 0.670827 nm)
> Warning: Long Bond (421-422 = 0.950023 nm)
> Warning: Long Bond (422-424 = 0.717385 nm)
> Warning: Long Bond (424-425 = 1.08167 nm)
> Warning: Long Bond (426-428 = 0.511531 nm)
> Warning: Long Bond (426-431 = 1.08592 nm)
> Warning: Long Bond (432-433 = 0.912686 nm)
> Warning: Long Bond (432-435 = 0.519809 nm)
> Warning: Long Bond (435-436 = 0.450706 nm)
> Warning: Long Bond (436-439 = 0.325467 nm)
> Warning: Long Bond (439-441 = 0.719692 nm)
> Warning: Long Bond (439-456 = 0.856575 nm)
> Warning: Long Bond (441-442 = 0.700777 nm)
> Warning: Long Bond (442-444 = 0.617616 nm)
> Warning: Long Bond (442-458 = 0.526962 nm)
> Warning: Long Bond (444-445 = 0.608832 nm)
> Warning: Long Bond (444-454 = 0.466287 nm)
> Warning: Long Bond (447-449 = 0.719506 nm)
> Warning: Long Bond (449-453 = 0.400781 nm)
> Warning: Long Bond (454-455 = 0.781281 nm)
> Warning: Long Bond (456-458 = 0.43477 nm)
> Warning: Long Bond (456-461 = 0.854421 nm)
> Warning: Long Bond (431-432 = 1.14334 nm)
> Warning: Long Bond (462-463 = 0.675814 nm)
> Warning: Long Bond (462-464 = 0.429367 nm)
> Warning: Long Bond (462-465 = 0.92747 nm)
> Warning: Long Bond (465-466 = 0.61628 nm)
> Warning: Long Bond (466-469 = 0.813831 nm)
> Warning: Long Bond (469-471 = 0.829303 nm)
> Warning: Long Bond (471-472 = 1.0632 nm)
> Warning: Long Bond (472-474 = 0.990568 nm)
> Warning: Long Bond (472-490 = 0.419376 nm)
> Warning: Long Bond (474-475 = 0.864227 nm)
> Warning: Long Bond (474-487 = 0.382602 nm)
> Warning: Long Bond (475-477 = 0.851014 nm)
> Warning: Long Bond (477-478 = 0.683878 nm)
> Warning: Long Bond (478-479 = 0.68112 nm)
> Warning: Long Bond (478-487 = 0.707226 nm)
> Warning: Long Bond (479-480 = 0.608289 nm)
> Warning: Long Bond (479-483 = 0.619426 nm)
> Warning: Long Bond (483-484 = 0.608289 nm)
> Warning: Long Bond (486-487 = 0.72991 nm)
> Warning: Long Bond (488-490 = 0.500783 nm)
> Warning: Long Bond (488-493 = 0.852481 nm)
> Warning: Long Bond (461-462 = 0.80635 nm)
> Warning: Long Bond (494-495 = 0.509133 nm)
> Warning: Long Bond (494-496 = 0.836758 nm)
> Warning: Long Bond (494-497 = 0.316253 nm)
> Warning: Long Bond (497-498 = 0.728011 nm)
> Warning: Long Bond (501-503 = 0.5657 nm)
> Warning: Long Bond (501-518 = 0.813968 nm)
> Warning: Long Bond (503-504 = 0.252367 nm)
> Warning: Long Bond (504-506 = 0.608967 nm)
> Warning: Short Bond (504-520 = 0.038 nm)
> Warning: Long Bond (506-507 = 0.644884 nm)
> Warning: Long Bond (506-516 = 0.860828 nm)
> Warning: Long Bond (507-509 = 0.413068 nm)
> Warning: Long Bond (509-511 = 0.376962 nm)
> Warning: Long Bond (511-512 = 0.361055 nm)
> Warning: Long Bond (511-515 = 0.652019 nm)
> Warning: Long Bond (515-516 = 1.1316 nm)
> Warning: Long Bond (516-517 = 0.912686 nm)
> Warning: Long Bond (518-523 = 0.769769 nm)
> Warning: Long Bond (493-494 = 0.901619 nm)
> Warning: Long Bond (524-525 = 0.945918 nm)
> Warning: Long Bond (524-527 = 0.334162 nm)
> Warning: Long Bond (527-528 = 0.92624 nm)
> Warning: Long Bond (531-533 = 0.674158 nm)
> Warning: Long Bond (531-546 = 0.322639 nm)
> Warning: Long Bond (533-534 = 0.905884 nm)
> Warning: Long Bond (534-536 = 0.709384 nm)
> Warning: Long Bond (534-548 = 0.448357 nm)
> Warning: Long Bond (536-537 = 0.644884 nm)
> Warning: Long Bond (536-544 = 0.721416 nm)
> Warning: Long Bond (539-540 = 0.943517 nm)
> Warning: Long Bond (540-541 = 1.14404 nm)
> Warning: Long Bond (540-542 = 0.957414 nm)
> Warning: Long Bond (542-544 = 0.415655 nm)
> Warning: Long Bond (544-545 = 0.549837 nm)
> Warning: Long Bond (546-548 = 0.731762 nm)
> Warning: Long Bond (546-551 = 0.87139 nm)
> Warning: Long Bond (523-524 = 0.81204 nm)
> Warning: Long Bond (552-553 = 0.614348 nm)
> Warning: Long Bond (552-554 = 0.321685 nm)
> Warning: Long Bond (552-555 = 0.721166 nm)
> Warning: Long Bond (555-556 = 0.825959 nm)
> Warning: Long Bond (556-559 = 0.282929 nm)
> Warning: Long Bond (559-561 = 0.383275 nm)
> Warning: Long Bond (559-574 = 0.362062 nm)
> Warning: Long Bond (561-562 = 0.700874 nm)
> Warning: Long Bond (562-576 = 0.611955 nm)
> Warning: Long Bond (564-565 = 0.453625 nm)
> Warning: Long Bond (564-572 = 0.32187 nm)
> Warning: Long Bond (565-567 = 0.614781 nm)
> Warning: Long Bond (567-568 = 0.924608 nm)
> Warning: Long Bond (568-569 = 0.863067 nm)
> Warning: Long Bond (568-570 = 0.810385 nm)
> Warning: Long Bond (570-572 = 0.582275 nm)
> Warning: Long Bond (572-573 = 0.709908 nm)
> Warning: Long Bond (574-576 = 0.732913 nm)
> Warning: Long Bond (574-579 = 0.331662 nm)
> Warning: Long Bond (551-552 = 0.911265 nm)
> Warning: Long Bond (580-581 = 0.9597 nm)
> Warning: Long Bond (580-582 = 0.722773 nm)
> Warning: Long Bond (580-583 = 0.7294 nm)
> Warning: Long Bond (583-584 = 0.442579 nm)
> Warning: Long Bond (584-587 = 0.360605 nm)
> Warning: Long Bond (587-589 = 0.719506 nm)
> Warning: Long Bond (587-604 = 0.583288 nm)
> Warning: Long Bond (589-590 = 0.852015 nm)
> Warning: Long Bond (590-592 = 0.516124 nm)
> Warning: Long Bond (592-593 = 0.761609 nm)
> Warning: Long Bond (595-597 = 0.929223 nm)
> Warning: Long Bond (597-598 = 0.815255 nm)
> Warning: Short Bond (597-601 = 0.00600001 nm)
> Warning: Long Bond (601-602 = 0.379685 nm)
> Warning: Long Bond (602-603 = 0.5001 nm)
> Warning: Long Bond (604-606 = 0.520047 nm)
> Warning: Long Bond (604-609 = 0.764519 nm)
> Warning: Long Bond (579-580 = 0.828788 nm)
> Warning: Long Bond (610-611 = 0.435211 nm)
> Warning: Long Bond (610-613 = 0.720833 nm)
> Warning: Long Bond (613-614 = 0.612406 nm)
> Warning: Long Bond (614-617 = 0.598071 nm)
> Warning: Long Bond (617-619 = 0.728288 nm)
> Warning: Long Bond (617-634 = 0.948709 nm)
> Warning: Long Bond (620-636 = 0.830906 nm)
> Warning: Long Bond (622-623 = 0.322639 nm)
> Warning: Long Bond (622-632 = 0.683492 nm)
> Warning: Long Bond (623-625 = 0.907659 nm)
> Warning: Long Bond (625-627 = 0.433849 nm)
> Warning: Long Bond (627-631 = 0.503829 nm)
> Warning: Long Bond (631-632 = 0.366191 nm)
> Warning: Long Bond (634-636 = 0.645046 nm)
> Warning: Long Bond (634-639 = 0.405408 nm)
> Warning: Long Bond (609-610 = 0.31805 nm)
> Warning: Long Bond (640-641 = 0.949004 nm)
> Warning: Long Bond (640-642 = 0.302655 nm)
> Warning: Long Bond (643-644 = 0.7245 nm)
> Warning: Long Bond (644-647 = 0.722225 nm)
> Warning: Long Bond (647-649 = 0.808923 nm)
> Warning: Long Bond (647-667 = 0.361565 nm)
> Warning: Long Bond (649-650 = 0.710563 nm)
> Warning: Long Bond (650-652 = 1.14018 nm)
> Warning: Long Bond (650-669 = 0.367098 nm)
> Warning: Long Bond (652-653 = 0.990257 nm)
> Warning: Long Bond (652-666 = 0.458477 nm)
> Warning: Long Bond (653-655 = 0.707661 nm)
> Warning: Long Bond (655-656 = 0.525967 nm)
> Warning: Long Bond (656-657 = 0.544875 nm)
> Warning: Long Bond (656-666 = 0.414981 nm)
> Warning: Long Bond (657-658 = 0.500529 nm)
> Warning: Long Bond (661-662 = 0.514669 nm)
> Warning: Long Bond (661-665 = 0.431017 nm)
> Warning: Long Bond (665-666 = 0.462775 nm)
> Warning: Long Bond (667-669 = 0.501597 nm)
> Warning: Long Bond (673-674 = 0.361641 nm)
> Warning: Long Bond (673-675 = 0.508759 nm)
> Warning: Long Bond (673-676 = 0.836254 nm)
> Warning: Long Bond (676-677 = 0.331362 nm)
> Warning: Long Bond (677-680 = 0.737835 nm)
> Warning: Long Bond (680-682 = 1.14054 nm)
> Warning: Long Bond (680-700 = 0.922697 nm)
> Warning: Long Bond (682-683 = 0.501597 nm)
> Warning: Long Bond (683-685 = 0.506679 nm)
> Warning: Long Bond (683-702 = 0.761725 nm)
> Warning: Long Bond (685-686 = 0.957961 nm)
> Warning: Long Bond (686-688 = 0.861357 nm)
> Warning: Long Bond (688-689 = 0.460783 nm)
> Warning: Long Bond (689-690 = 0.424566 nm)
> Warning: Long Bond (690-691 = 0.4325 nm)
> Warning: Long Bond (690-692 = 0.553986 nm)
> Warning: Long Bond (692-694 = 0.812779 nm)
> Warning: Long Bond (694-695 = 0.681469 nm)
> Warning: Long Bond (694-698 = 0.806331 nm)
> Warning: Long Bond (700-702 = 0.895366 nm)
> Warning: Long Bond (700-705 = 0.346238 nm)
> Warning: Long Bond (672-673 = 0.44989 nm)
> Warning: Long Bond (706-707 = 0.328513 nm)
> Warning: Long Bond (709-710 = 0.711179 nm)
> Warning: Long Bond (710-713 = 0.638548 nm)
> Warning: Long Bond (713-715 = 0.45449 nm)
> Warning: Long Bond (713-728 = 0.543177 nm)
> Warning: Long Bond (715-716 = 0.728187 nm)
> Warning: Long Bond (716-718 = 0.553986 nm)
> Warning: Long Bond (716-730 = 0.826259 nm)
> Warning: Long Bond (718-719 = 0.512173 nm)
> Warning: Long Bond (718-726 = 0.707141 nm)
> Warning: Long Bond (719-721 = 0.578692 nm)
> Warning: Long Bond (721-722 = 0.316583 nm)
> Warning: Long Bond (722-723 = 0.413807 nm)
> Warning: Long Bond (722-724 = 0.912938 nm)
> Warning: Long Bond (724-726 = 0.325 nm)
> Warning: Long Bond (726-727 = 0.910719 nm)
> Warning: Long Bond (728-730 = 0.864324 nm)
> Warning: Long Bond (728-733 = 0.719322 nm)
> Warning: Long Bond (734-735 = 0.835924 nm)
> Warning: Long Bond (734-736 = 0.503353 nm)
> Warning: Long Bond (734-737 = 0.51 nm)
> Warning: Long Bond (737-738 = 0.361288 nm)
> Warning: Long Bond (738-741 = 0.608297 nm)
> Warning: Long Bond (741-743 = 1.13952 nm)
> Warning: Long Bond (741-758 = 0.406079 nm)
> Warning: Long Bond (743-744 = 0.608639 nm)
> Warning: Long Bond (744-746 = 0.646913 nm)
> Warning: Long Bond (744-760 = 0.729756 nm)
> Warning: Long Bond (746-747 = 0.632911 nm)
> Warning: Long Bond (746-756 = 0.33289 nm)
> Warning: Long Bond (747-749 = 0.612679 nm)
> Warning: Long Bond (749-751 = 0.860828 nm)
> Warning: Long Bond (751-752 = 0.644885 nm)
> Warning: Long Bond (751-755 = 0.566153 nm)
> Warning: Long Bond (755-756 = 0.431133 nm)
> Warning: Long Bond (756-757 = 0.413068 nm)
> Warning: Long Bond (758-760 = 0.619052 nm)
> Warning: Long Bond (733-734 = 0.61628 nm)
> Warning: Long Bond (764-765 = 0.732735 nm)
> Warning: Long Bond (764-767 = 0.322248 nm)
> Warning: Long Bond (767-768 = 0.501597 nm)
> Warning: Long Bond (768-771 = 0.327194 nm)
> Warning: Long Bond (771-773 = 0.653979 nm)
> Warning: Long Bond (771-790 = 0.450706 nm)
> Warning: Long Bond (773-774 = 0.608875 nm)
> Warning: Long Bond (774-792 = 0.434161 nm)
> Warning: Long Bond (776-777 = 0.633537 nm)
> Warning: Long Bond (776-789 = 0.793123 nm)
> Warning: Long Bond (777-779 = 0.519809 nm)
> Warning: Long Bond (779-780 = 0.789015 nm)
> Warning: Long Bond (780-781 = 0.720447 nm)
> Warning: Long Bond (781-782 = 0.540926 nm)
> Warning: Long Bond (781-785 = 0.676184 nm)
> Warning: Long Bond (785-786 = 0.63459 nm)
> Warning: Long Bond (786-788 = 0.613294 nm)
> Warning: Long Bond (788-789 = 0.420386 nm)
> Warning: Long Bond (790-792 = 0.50636 nm)
> Warning: Long Bond (763-764 = 0.374979 nm)
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
>
> WARNING: atom P is missing in residue DT 1 in the pdb file
>
>
> WARNING: atom O1P is missing in residue DT 1 in the pdb file
>
>
> WARNING: atom O2P is missing in residue DT 1 in the pdb file
>
>
> WARNING: atom C7 is missing in residue DT 1 in the pdb file
>
>
> WARNING: atom H71 is missing in residue DT 1 in the pdb file
> You might need to add atom H71 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H72 is missing in residue DT 1 in the pdb file
> You might need to add atom H72 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H73 is missing in residue DT 1 in the pdb file
> You might need to add atom H73 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom C7 is missing in residue DT 11 in the pdb file
>
>
> WARNING: atom H71 is missing in residue DT 11 in the pdb file
> You might need to add atom H71 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H72 is missing in residue DT 11 in the pdb file
> You might need to add atom H72 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H73 is missing in residue DT 11 in the pdb file
> You might need to add atom H73 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom C7 is missing in residue DT 13 in the pdb file
>
>
> WARNING: atom H71 is missing in residue DT 13 in the pdb file
> You might need to add atom H71 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H72 is missing in residue DT 13 in the pdb file
> You might need to add atom H72 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H73 is missing in residue DT 13 in the pdb file
> You might need to add atom H73 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom P is missing in residue DA 14 in the pdb file
>
>
> WARNING: atom O1P is missing in residue DA 14 in the pdb file
>
>
> WARNING: atom O2P is missing in residue DA 14 in the pdb file
>
>
> WARNING: atom C7 is missing in residue DT 18 in the pdb file
>
>
> WARNING: atom H71 is missing in residue DT 18 in the pdb file
> You might need to add atom H71 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H72 is missing in residue DT 18 in the pdb file
> You might need to add atom H72 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H73 is missing in residue DT 18 in the pdb file
> You might need to add atom H73 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom C7 is missing in residue DT 19 in the pdb file
>
>
> WARNING: atom H71 is missing in residue DT 19 in the pdb file
> You might need to add atom H71 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H72 is missing in residue DT 19 in the pdb file
> You might need to add atom H72 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H73 is missing in residue DT 19 in the pdb file
> You might need to add atom H73 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom C7 is missing in residue DT 24 in the pdb file
>
>
> WARNING: atom H71 is missing in residue DT 24 in the pdb file
> You might need to add atom H71 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H72 is missing in residue DT 24 in the pdb file
> You might need to add atom H72 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> WARNING: atom H73 is missing in residue DT 24 in the pdb file
> You might need to add atom H73 to the hydrogen database of
> residue DT
> in the file ff???.hdb (see the manual)
>
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.3
> Source code file: pdb2top.c, line: 704
>
> Fatal error:
> There were 30 missing atoms in molecule Protein_A, if you want to use
> this incomplete topology anyhow, use the option -missing
> -------------------------------------------------------
>
> "Does All This Money Really Have To Go To Charity ?" (Rick
> so if anyone have idea about this please suggest me can I use missing
> option for further processing .
> or If it will make harm to simulation process please suggest me
> something to solve this long bond problem.
>
> Thanking you
> Nitu sharma.
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
>
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