http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php CHARMM forums: parameter sets CHARMM Forums - UBB.threads(tm) http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27876#Post27876 Posted by lennart:
paras? Please forgive me the following, not directed at you specifically. Plz uz prpr nglsh whn pstng! Lab and internet jargon is to be avoided, always. Period. This is not a chat among a local group of friends with access only to iDevices. A few ]]> Fri, 08 Jul 2011 17:43:08 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27860#Post27860 Posted by xiaobo:
Could you send me the SAH parameters to my email adress wanxiaobo@nibs.ac.cn , I would how to add the reasonable charges of SAM based on the SAH. ]]> Wed, 06 Jul 2011 07:44:54 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27857#Post27857 Posted by JohnPenniston:
Does anyone know of a set of parameters for an aspartyl phosphate residue? The side-chain carboxyl of an aspartate is phosphorylated to form a high-energy mixed anhydride in the reaction cycle of the P-type ATPases. This is what I need to model, so e]]> Tue, 05 Jul 2011 21:47:32 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27811#Post27811 Posted by poker:
The fragment in (2) is (4-methylphenyl)phosphonate according to Chemspider. From there I guess I can try to find its likely ionic state. I'm growing to love that site... [i]Edit:[/i] Dang, the logD values are blank. It seems like I can't get to a ]]> Thu, 30 Jun 2011 04:42:25 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27796#Post27796 Posted by Jon Phillips:
Haha! Found it! In case anybody else has this problem, it's at [url]http://dogmans.umaryland.edu/~kenno/tutorial/do_remas[/url] also [url]http://dogmans.umaryland.edu/~kenno/tutorial/rm_pyrrolidine_remas[/url] and [url]http://dogmans.umaryland.ed]]> Wed, 29 Jun 2011 09:30:35 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27739#Post27739 Posted by apredeus:
Hello all, I have a general question. Whenever Zn ion is bound to a histidine, does HIS always remain neutral in biological systems? There certainly are complexes with deprotonated imidazoles and most transition metals, but it seems that most of ]]> Fri, 24 Jun 2011 17:43:45 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27713#Post27713 Posted by hiva:
Oops! right, thanks It was good to know the difference between sigma and Rmin ]]> Tue, 21 Jun 2011 11:12:08 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27614#Post27614 Posted by mltan:
Hi all, I am going to simulate liquid methane, but can not find any parmeters in the parameter file. I wonder if there is any parameter available in CHARMM or do you have any suggestion for it? Thanks, Ming ]]> Mon, 06 Jun 2011 16:17:16 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27603#Post27603 Posted by rmv:
It is not possible to answer that based on the information provided so far. The IC PARAM message implies that BOND and/or ANGLE terms are missing. It is likely that there will be missing DIHEDRAL terms as well. Making the list I suggested should h]]> Thu, 02 Jun 2011 15:47:24 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27574#Post27574 Posted by lennart:
It is "you", not "u"... The process in itself is correct, but that is not enough. The contents of the files also have to be correct: All the MASS statements have to be in the first RTF you read. (This requirement is relaxed with the flexible par]]> Sat, 28 May 2011 09:25:16 CDT