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#938 - 02/15/04 01:34 AM force field compatibility
shouqinlv Offline
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Registered: 02/15/04
Posts: 30
Loc: BeiJing, China
Hi, all,
Help!
I am trying to do the molecular dynamics simulation of a protein complex using the program NAMD. Unfortunately, because of the including of small suger part and a abnormal sulfated amino acid in the complex, and the lacking of the topology and parameter files of the suger part and the abnormal amono acid in CHARMM force field, the simulations can’t go on smoothly. Incidentally, I found the force field files “toph3.cho, param3.cho” for the suger part, and “top.so4, param.so4” for SO42- in XPLOR, and especially the remarks of “toph3.cho, param3.cho” are that they can be used with CHARMM19 protein parameters, then I take it for granted that they can be used with CHARMM22 protein parameters too.
So, ignore of the emphasizing of “toph3.cho, param3.cho” for “structure refinement”, I want to do the molecular dynamics simulation of my protein complex with cooperated force field files, i.e. CHARMM22 for the protein part of the complex, “toph3.cho, param2.cho” for the suger part of the complex, and the combination of CHARMM22 and “top.so4, param.so4” for the abnormal amino acid.
Now, the simulations can go. But, whether is the cooperation feasible or not? How can I prove the feasibility? If not, How can I solve this problem better? Did you meet this kind of difficulty in your work, and would you please give your judgement in your convenience? Thank you very much!


Edited by alex (03/11/04 06:02 PM)

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#939 - 02/15/04 05:17 PM Re: questions about force field cooperation [Re: shouqinlv]
rmv Online   content

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Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
CHARMM19 and CHARMM22 parameter sets are not compatible, and represent a major change in how molecules are represented; the former uses extended (a.k.a. united) atom types where aliphatic protons are not explicitly represented, but incorporated into the C atom by increasing the mass and adjusting the VDW radii to reflect volumes for neutral -CH2-, -CH3, etc.

CHARMM22 and later parameter sets represent all the H atoms explicitly.

I would advise against trying to combine old X-PLOR parameter sets with CHARMM22 and CHARMM27 parameter sets. You may need to add some new residues yourself to supplement what's provided, which isn't that difficult, as long as no new functional groups are needed.

Have you looked thru the combined protein and nucleic acid topology and parameter files?
_________________________
Rick Venable
computational chemist


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#940 - 02/15/04 09:31 PM Re: Re: questions about force field cooperation [Re: rmv]
shouqinlv Offline
Forum Member

Registered: 02/15/04
Posts: 30
Loc: BeiJing, China
Thanks! Is it OK to combine the old XPLOR parameter sets with CHARMM19 for molecular dynamics simulation? My lack is some “sugar” part (for example, FUC: fucose; SIA:O-SIALIC ACID; GAL:D-GALACTOSE; NAG:N-ACETYL-D-GLUCOSAMINE; NGA:N-ACETYL-D-GALACTOSAMINE) and a abnormal amino acid (TYS: sulfated tyrosine), I did not find the similar parameter sets as reference for the “sugar” part except for “toph3.cho, param3.cho”, and “top.so4, param.so4” for SO42-. And I am attracted by the remarks of “toph3.cho, param3.cho” that they can be combined with CHARMM19 protein parameters, but unfortunately, these parameter sets are emphasized that they are for x-ray structure determination (what’s the difference between the general force field parameter sets and those for structure determination?). would you please give me some more suggestion?

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#941 - 02/17/04 10:49 AM Re: questions about force field cooperation [Re: shouqinlv]
alex Offline

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Registered: 10/04/03
Posts: 780
there are parameters for most of the molecules you
need in charmm22/27, but it will take some mixing and
matching. there are parameters for glucose in the
sugar toppar file and for sulfate in the lipid toppar
files. as to the variety of sugar you are interested
you will have to modify the glucose accordingly.
note that this is risky as the transferability of
parameters, especially the dihedral terms, is
limited in empirical force fields. thus, you should
do some QM calculations to verify the location
of minima for the rotatable bonds you create.

you can get examples of the parameter process from
my web page.

alex

http://www.pharmacy.umaryland.edu/faculty/amackere/
_________________________
School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

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#942 - 02/18/04 02:38 AM Re: Re:Re: questions about force field cooperation [Re: alex]
shouqinlv Offline
Forum Member

Registered: 02/15/04
Posts: 30
Loc: BeiJing, China
Thanks! Unfortunately, it seems that it is impossible to avoid the QM calculations in order to get complete parameter sets. Before that, need your more help.
1) What’s the difference between “top_all22_prot.inp” and “top_all22_prot_lipid.inp”, or between “par_all22_prot.inp” and “par_all22_prot_lipid.inp”? just simple combination?
2) Is it feasible to combine the “top/par_all22_suger.inp” and “top/par_all22_prot_lipid.inp”?
3) what’s the difference between IC(internal coordinate) of topology file and dihedral or improper parameters? Does the IC have precedence over general dihedral or improper parameters in calculations?
4) How to get the parameter set of some glycoside bonds, e.g. alpha 1-3, beta 1-6, et al, and O-LINK? QM calculations again?
5) What’s the difference between CHARMM format and XPLOR format of force field parameter sets? Can they be exchanged automatically?
Thanks a lot!
Shouqin Lv

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