Topic Options
#8632 - 10/25/05 11:16 AM Heme parameters (C - CPB bond)
rxj Offline
Forum Member

Registered: 10/24/05
Posts: 3
Loc: Boulder CO
I'm using NAMD to set up a simulation with CHARMM parameters. I built the heme protein using the topology file top_all27_prot_lipid.inp and tried running the simulation with the parameter file par_all22_prot.inp
The heme in my system and the one in the topology file are exactly the same molecule.

Unfortunately, NAMD complains about missing parameters for the C-CPB bond. I've examined the heme PSF and PDB files, and I don't see anything out of order. When I looked at the parameter file, I did not find C-CPB bond parameters.

How should I proceed? Do I need to relabel some atoms?

Thanks.

Ralph

Top
#8633 - 10/26/05 11:42 AM Re: Heme parameters (C - CPB bond) [Re: rxj]
alex Offline

Forum Member

Registered: 10/04/03
Posts: 780

as there is no atom with a C atom type in Heme, i'm not sure what the problem is. are you trying to put different substituents on the heme? carefully check the atom types in the original charmm file as well as the files you are using for NAMD. also, be sure you are using the same topology and parameter files throughout; the atom numbers assigned in the MASS list in the topology identify atom types with internal parameters. if a different MASS list is used with a previously generated PSF, there will be problems with atom types.

alex
_________________________
School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

Top
#8634 - 10/27/05 12:00 PM Re: Heme parameters (C - CPB bond) [Re: alex]
rxj Offline
Forum Member

Registered: 10/24/05
Posts: 3
Loc: Boulder CO
The heme in my system is the same one referred to as "RESI HEME -2.00 ! 6-liganded planar heme" in the topology file I used (top_all27_prot_lipid.inp). It's not modified in any way.
For some reason, atoms on the vinyl subsituents (CAC, CBC, CAB, and CBB) are being identified as "C"

I think the topology file does identify "C" atoms for the heme residue. I might be misinterpreting it, but here are the lines which do it:

GROUP
ATOM CAB C -0.20
ATOM HAB HA 0.20
GROUP
ATOM CBB C -0.20
ATOM HBB1 HA 0.10
ATOM HBB2 HA 0.10
GROUP
ATOM CMC CT3 -0.27
ATOM HMC1 HA 0.09
ATOM HMC2 HA 0.09
ATOM HMC3 HA 0.09
GROUP
ATOM CAC C -0.20
ATOM HAC HA 0.20
GROUP
ATOM CBC C -0.20
ATOM HBC1 HA 0.10
ATOM HBC2 HA 0.10

Which atom type should I find for those four?

Top
#8635 - 10/31/05 09:00 PM Re: Heme parameters (C - CPB bond) [Re: rxj]
alex Offline

Forum Member

Registered: 10/04/03
Posts: 780

there is something wrong with the heme atom types; go to my web page and get the c31b1 release of the toppar files and use those. note that the heme parameters are in the stream subdirectory (see the first post of this discussion for details).

http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm

alex
_________________________
School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

Top
#8636 - 11/05/05 12:01 AM Re: Heme parameters (C - CPB bond) [Re: alex]
rxj Offline
Forum Member

Registered: 10/24/05
Posts: 3
Loc: Boulder CO
Indeed, that fixed it. Apparently the topology file included with VMD 1.8.3 distribution was corrupted.
Thanks.
Ralph

Top

Moderator:  alex, chmgr, John Legato