[gmx-users] Cannot Generate CHARMM36 Topology for POPC with Virtual Sites
Prajapati, Jigneshkumar Dahyabhai
j.prajapati at jacobs-university.de
Wed May 21 20:35:24 CEST 2014
Dear Justin,
I am facing the same problem and only difference is that I am using POPE lipids. I am using GROMACS 4.6.5 and error exists for in built CHARMM27 and CHARMM36 march release. Parameters are missing for following atomtypes.
MNH3 CTL2
MCH3 CTL2
I have gone through the ff files and I found something as following.
The section of ffbonded.itp file of CHARMM36 is,
-------------------------------------------------------------------------------
[ constrainttypes ]
; this section is copied from OPLS. In theory we could recalculate
; optimal geometries from charmm values, but since pratical equilibrium
; geometries do not correspond exactly to these values anyway it is not
; worth the effort...
#ifdef HEAVY_H
; account for larger inertia with heavy hydrogens
; constraints for the rigid NH3 groups
MNH3 CT1 2 0.191406
MNH3 CT2 2 0.191406
MNH3 CT3 2 0.191406
MNH3 MNH3 2 0.165238
; constraints for rigid ch3
MCH3 CT1 2 0.206892
MCH3 CT2 2 0.206000
MCH3 CT3 2 0.206179
MCH3 MCH3 2 0.185689
MCH3 S 2 0.233335
#else
; no heavy hydrogens.
; constraints for the rigid NH3 groups
MNH3 CT1 2 0.159603
MNH3 CT2 2 0.159603
MNH3 CT3 2 0.159603
MNH3 MNH3 2 0.082619
; constraints for rigid ch3
MCH3 CT1 2 0.168122
MCH3 CT2 2 0.167162
MCH3 CT3 2 0.167354
MCH3 MCH3 2 0.093582
MCH3 S 2 0.195314
#endif
-------------------------------------------
In above section we can see that the parameters for "CT2" is present which is "aliphatic sp3 C for CH2" and it belongs to "proteins"
MNH3 CT2 2 0.191406
MCH3 CT2 2 0.206000
The atomtype "CTL2 " is for "carbon of methylene group (-CH2-)" and it belong to "lipid".
According to atom type definitions, both carbons are same but belongs to different residues. I have not tested by adding the values (will be done soon).
So, the question is that can I use CT2 parameters for CTL2 atomtype?
Thank you
-Jignesh
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Tuesday, April 08, 2014 9:37 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Cannot Generate CHARMM36 Topology for POPC with Virtual Sites
On 4/8/14, 12:45 PM, Chris Ing wrote:
> I'm trying to build a charmm36.ff topology file for a POPC with virtual
> sites. In GROMACS 4.5.5 and 4.6.3 (with the most recent CHARMM36 March
> 2014), when I run:
>
> pdb2gmx -f POPC.pdb -o POPC.gro -p POPC.top -i POPC.posre -vsite hydrogen
> grompp -f empty.mdp -c POPC.gro -p POPC.top -o test.tpr
>
> I get multiple constraint errors:
>
> ERROR 1 [file POPC.top, line 311]:
>
> No default Constr. No Conn. types
>
> Which is due to the lack of two constraints not in ffbonded.itp:
>
> MCH3 NTL
> MCH3 CTL2
>
> MCH3 is the virtual site of a CH3 group, and NTL refers to the choline
> nitrogen in the POPC headgroup and CTL2, in this case, is the carbon
> closest to the CH3 group on the POPC tail.
>
> The same question was asked in the gmx-users thread "amber99sb_virtual site
> lipids dopc MCH3_N constraint types" by Song Ke, where the reply from Erik
> Marklund was to manually add this value "from bond lengths, center of mass
> for the group and the moment of inertia.". In lieu of wiping an inch of
> dust off my classical mechanics textbook, I wondered if I could copy some
> additional constraint values from the OPLS ffbonded.itp file.
>
> The charmm36.ff ffbonded.itp file states that the constrainttypes section
> is copied directly from OPLS (the restraint values are slightly adjusted?).
> Yet, many entries were not copied from OPLS to CHARMM36:
>
> OPLS:
>
> MNH3 CT_2 2 0.158255
> MNH3 MNH3 2 0.080236
> MCH3A C 2 0.166040
> MCH3A C_2 2 0.166040
> MCH3A CW 2 0.164312
> MCH3A CV 2 0.164312
> MCH3A CS 2 0.163448
> MCH3A CA 2 0.164888
> MCH3A CB 2 0.164888
> MCH3A N 2 0.159040
> MCH3A S 2 0.193874
> MCH3A MCH3A 2 0.092160
> MCH3B CT 2 0.167031
> MCH3B CT_2 2 0.167031
> MCH3B CT_3 2 0.167031
> MCH3B CO 2 0.167031
> MCH3B MCH3B 2 0.091456
>
> CHARMM36:
>
> MNH3 CT3 2 0.159603
> MNH3 MNH3 2 0.082619
> MCH3 CT1 2 0.168122
> MCH3 CT2 2 0.167162
> MCH3 CT3 2 0.167354
> MCH3 S 2 0.195314
> MCH3 MCH3 2 0.093582
>
> Would it be acceptable to use these OPLS constraint values in CHARMM36 to
> resolve my problem?:
>
> MCH3A N 2 0.159040
> MCH3B CT 2 0.167031
>
> Thanks gmx-users/Justin Lemkul!
>
For what it's worth, we have done exactly zero testing with virtual sites. The
sections of text you are referring to were copied basically verbatim from what
was distributed as charmm27.ff in Gromacs prior to our creation of charmm36.ff.
I don't know if that's of any use, but please consider it at least a strong
disclaimer :)
> -Chris
>
> P.S. I had similar missing dihedral/ub errors when trying to build my
> charmm36.ff protein topology with virtual sites whenever I used a neutral
> terminus. I didn't look into the details because using a charged terminus,
> I had no errors.
>
If you can provide me with specific errors and the atomtypes to which they
correspond, I will look into it. We recently fixed a problem with missing U-B
types for neutral termini with branched-chain amino acids, but the necessary
parameters were added before our March release. To my knowledge, that issue
should be resolved, but if there are remaining problems, I'd be happy to look
into it. If it only occurs when using virtual sites, again, that's because we
never looked into it.
-Justin
--
==================================================
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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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