On 4/1/14, 8:49 AM, Ahmet yıldırım wrote:
There are both Zn-OH(zinc-hydroxyl) and Zn-H2O (zinc-water) bond in
structure, then should I modify "aminoacids.hdb" and "aminoacids.rtp" to
add OH (hydroxyl) and water parameters?
The parameters listed in Table 1 need to be added to ffbonded.itp and
ffnonbonded.itp. The thing to watch out for is that there are two different
H-O-H angles that are defined, depending on whether the water is free or bound
to Zn. Therefore, you need unique atomtypes to differentiate between different
types of water, so that requires modification of atomtypes.atp, as well, if you
will be processing the structure with pdb2gmx.
Table 2 corresponds to a specific residue that needs to be added as an .rtp
entry (again, only if you are using pdb2gmx to create the topology). The .hdb
entry is only necessary if you do not have H positions in the input coordinate file.
-Justin
2014-04-01 11:03 GMT+03:00 Ahmet yıldırım <ahmedo...@gmail.com>:
Firstly, I will change ffnonbonded.itp and ffbonded.itp. Later?
2014-04-01 10:37 GMT+03:00 Ahmet yıldırım <ahmedo...@gmail.com>:
Dear users,
Please see the file from the link:
http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F%2Fpubmedcentralcanada.ca%2Fpicrender.cgi%3Fartinstid%3D1482211%26blobname%3DNIHMS61946-supplement-File002.pdf&ei=DGs6U560PMHxhQejyIDABg&usg=AFQjCNGUfMCQZYegoRpLGg5D9GjpFsPCxQ&sig2=vr6-1syRClNsDmFdMlWyXw&bvm=bv.63934634,d.ZG4
I want to add table 1 and table 2 parameters to amber force field. How can
I achieve it?
--
Ahmet Yıldırım
--
Ahmet Yıldırım
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
