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<br><br><br><br>Hi,<br>Thanks for the your reply. I quite know that there is need for expertise to be able to derive parameters, that's why i want to know if anyone already have the gromos parameters for the oxy- and carbomonoxy- heme.<br>The references i've seen so far for related works in my literature search used the charmm force field parameters and amber but again i had problems when i try to use amber, pdb2gmx complain of not finding residue heme in the topology file.<br>The question now is can i use charmm force field parameters in gromacs and how do i go about incorporating charmm ff into gromacs. <br>Please i need a guide because i'm relatively new in simulation work, i am from experimental background.<br>thanks. <br><br>> Message: 5<br>> Date: Tue, 27 Oct 2009 13:36:49 -0400<br>> From: "Justin A. Lemkul" <jalemkul@vt.edu><br>> Subject: Re: [gmx-users] Gromos Parameters for Heme bound Oxygen<br>> To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> Message-ID: <4AE72FB1.5020602@vt.edu><br>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>> <br>> <br>> <br>> Olaniyi Yusuff wrote:<br>> > Dear gmx users,<br>> > I would like to know if any one has parameters for oxygen or <br>> > carbonmonoxide bound to the heme in hemoglobin.<br>> > I am running MD simulations on hemoglobin using the gromos force field <br>> > G43a1 in gromacs, i had no problem when i used the pdb structure for <br>> > pure hemoglobin, but when i try to convert the pdb structure files for <br>> > the liganded hemoglobin (both oxy- and carbonmonoxy- ), there was <br>> > complain of my oxy and carbomonoxy residue unknown i.e not defined in <br>> > the .rtp file.<br>> > so i would like to know if there is anyone with parameters for these <br>> > kind of heme in gromacs or better still another reference of force field <br>> > with parameters for them that can be use in gromacs.<br>> > <br>> <br>> If it has been published, then perhaps the authors of that particular study will <br>> share them with you. If not, then realize what you are trying to do is <br>> certainly an expert topic, one that is not addressed easily:<br>> <br>> http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species<br>> <br>> -Justin<br>> <br>> > Thanks<br><br><br> <br /><hr />Windows Live: <a href='http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_3:092010' target='_new'>Friends get your Flickr, Yelp, and Digg updates when they e-mail you.</a></body>
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