Re: [gmx-users] errors with charmm36 ?
Hi Justin and Hubert:
Many thanks for your kind pointing out. Are you using the new version of
CHARMM36? I am using the one from here:
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36_gmx_format_sep13.tgz
I opened the merged.rtp file within the charmm36.ff file and found:
[ POPC ]
[ atoms ]
N NTL -0.600 0
C12 CTL2 -0.100 1
H12AHL0.250 2
H12BHL0.250 3
C13 CTL5 -0.350 4
H13AHL0.250 5
H13BHL0.250 6
H13CHL0.250 7
C14 CTL5 -0.350 8
H14AHL0.250 9
H14BHL0.250 10
H14CHL0.250 11
C15 CTL5 -0.350 12
H15AHL0.250 13
H15BHL0.250 14
H15CHL0.250 15
C11 CTL2 -0.080 16
H11A HAL20.090 17
H11B HAL20.090 18
PPL1.500 19
O13 O2L -0.780 20
Here is the information in my system.pdb file:
CRYST1 68.504 68.504 100.000 90.00 90.00 90.00 P 1 1
ATOM 1 N POPCA 1 -23.882 12.660 22.550 1.00-19.80 MEMB
ATOM 2 C12 POPCA 1 -23.575 13.505 21.320 1.00-19.52 MEMB
ATOM 3 H12A POPCA 1 -22.869 12.963 20.709 1.00 0.00 MEMB
ATOM 4 H12B POPCA 1 -23.032 14.387 21.628 1.00 0.00 MEMB
ATOM 5 C13 POPCA 1 -24.769 11.520 22.190 1.00-20.41 MEMB
ATOM 6 H13A POPCA 1 -24.241 10.891 21.490 1.00 0.00 MEMB
ATOM 7 H13B POPCA 1 -25.124 11.119 23.128 1.00 0.00 MEMB
ATOM 8 H13C POPCA 1 -25.638 11.934 21.700 1.00 0.00 MEMB
ATOM 9 C14 POPCA 1 -22.673 12.210 23.289 1.00-19.18 MEMB
ATOM 10 H14A POPCA 1 -23.025 11.888 24.257 1.00 0.00 MEMB
ATOM 11 H14B POPCA 1 -22.117 11.419 22.806 1.00 0.00 MEMB
ATOM 12 H14C POPCA 1 -21.935 12.981 23.456 1.00 0.00 MEMB
ATOM 13 C15 POPCA 1 -24.601 13.537 23.461 1.00-18.70 MEMB
ATOM 14 H15A POPCA 1 -24.979 13.080 24.364 1.00 0.00 MEMB
ATOM 15 H15B POPCA 1 -25.469 13.977 22.992 1.00 0.00 MEMB
ATOM 16 H15C POPCA 1 -23.953 14.351 23.749 1.00 0.00 MEMB
ATOM 17 C11 POPCA 1 -24.755 13.765 20.262 1.00-20.80 MEMB
ATOM 18 H11A POPCA 1 -24.458 14.498 19.482 1.00 0.00 MEMB
ATOM 19 H11B POPCA 1 -25.669 14.146 20.766 1.00 0.00 MEMB
ATOM 20 P POPCA 1 -24.213 11.984 18.366 1.00-18.20 MEMB
ATOM 21 O13 POPCA 1 -24.848 10.757 17.832 1.00-17.27 MEMB
ATOM 22 O14 POPCA 1 -22.825 11.910 18.814 1.00-18.67 MEMB
ATOM 23 O12 POPCA 1 -25.078 12.575 19.526 1.00-17.51 MEMB
The line 3 in merged.rtp and my .pdb file are H12a. The order seems to
be all right
thank you very much.
Albert
On 01/14/2014 02:55 PM, hubert santuz wrote:
Hi,
I just came across this issue a few days ago (with charmm-gui also).
In fact, atoms C13, C14 and C15 should be just after the C12 atoms in
the pdb (to match the itp file).
Here a piece of code that I used to retrieve the good order for all
POPC molecules in your gro file (on unix platform) :
for i in `grep POPC C13 yourfile.gro --line-number | awk -F:
'{print $1}'`
do
j=$((i-3))
(echo ${i}m${j}; echo w; echo q ) | ed yourfile.gro
done
Basically, ed is used to move each line POPC C13, 3 lines above. (6
lines for C14 and 9 lines for C15).
Beware also that a certain number of atom's name are wrong also :
0C21 (charmm-gui file) -- 'C210' (itp file)
1H10 -- 'H101'
etc.
In this case, 'sed' is a great tool ;)
Cheers,
Hubert
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Re: [gmx-users] errors with charmm36 ?
On 01/14/2014 04:12 PM, Justin Lemkul wrote: The .top is what matters, and your topology showed a clearly different order of atoms. Check the correspondence of the output configuration from pdb2gmx and the .top file. Inputs and .rtp entries are irrelevant once pdb2gmx is done working. -Justin Hi Justin: Many thanks for your helpful advices. The problem solved now. I some kind of mix the old c36 FF with the new one. I just update it in my system few days ago. thanks again for sugguestions. best Albert -- 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.
Re: [gmx-users] errors with charmm36 ?
I use this charmm36 (http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz, from Piggot et al, 2012, JCTC) which have slight differences in the order and in the name of few atoms compared to the one you used. So, everything I said concern only this version ;) Cheers, Hubert Le 14/01/2014 16:42, Albert a écrit : On 01/14/2014 04:12 PM, Justin Lemkul wrote: The .top is what matters, and your topology showed a clearly different order of atoms. Check the correspondence of the output configuration from pdb2gmx and the .top file. Inputs and .rtp entries are irrelevant once pdb2gmx is done working. -Justin Hi Justin: Many thanks for your helpful advices. The problem solved now. I some kind of mix the old c36 FF with the new one. I just update it in my system few days ago. thanks again for sugguestions. best Albert -- Hubert SANTUZ Equipe DSIMB UMR-S 665, INSERM-Paris Diderot, INTS 6 rue Alexandre Cabanel 75015 Paris Tel : 01 44 49 31 53 -- 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.
Re: [gmx-users] errors with charmm36 ?
On 1/14/14, 10:58 AM, hubert santuz wrote: I use this charmm36 (http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz, from Piggot et al, 2012, JCTC) which have slight differences in the order and in the name of few atoms compared to the one you used. So, everything I said concern only this version ;) I think it is probably worth emphasizing a point I have made previously, because I suspect there may be some confusion among the users out there. The tarball that can be downloaded from the website contains updated parameters for CHARMM36 lipids ONLY. The parameters in that distribution have outdated CHARMM22+CMAP parameters for proteins and CHARMM27 for nucleic acids (i.e. the files distributed as charmm27.ff in Gromacs). Users should not be led to believe that this tarball contains the full CHARMM36 force field, which is a different entity, available only from the MacKerell lab (note we will be uploading a new tarball soon that has updated parameters for CGenFF 2b8). -Justin Cheers, Hubert Le 14/01/2014 16:42, Albert a écrit : On 01/14/2014 04:12 PM, Justin Lemkul wrote: The .top is what matters, and your topology showed a clearly different order of atoms. Check the correspondence of the output configuration from pdb2gmx and the .top file. Inputs and .rtp entries are irrelevant once pdb2gmx is done working. -Justin Hi Justin: Many thanks for your helpful advices. The problem solved now. I some kind of mix the old c36 FF with the new one. I just update it in my system few days ago. thanks again for sugguestions. best Albert -- == Justin A. Lemkul, Ph.D. 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 == -- 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.
Re: [gmx-users] errors with charmm36 ?
It is good to know that the c36 and CGenFF is actively update. I just noticed that this new version c36 no longer contains classic TII3P water models: 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H 2: TIP4P TIP 4-point 3: TIP5P TIP 5-point 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None So in priciple, we have to use CHARMM TIP3P model, is it correct? I am always wondering, would it be better if there is a tool that could convert the output from paramchem websever into a single ligand.itp file? The parachem website can export the results including all known information from CGenFF related to target ligand. In such compelte output file, it contains all necessary information for a ligand parameters and toplogy thank you very much Albert On 01/14/2014 05:14 PM, Justin Lemkul wrote: I think it is probably worth emphasizing a point I have made previously, because I suspect there may be some confusion among the users out there. The tarball that can be downloaded from the website contains updated parameters for CHARMM36 lipids ONLY. The parameters in that distribution have outdated CHARMM22+CMAP parameters for proteins and CHARMM27 for nucleic acids (i.e. the files distributed as charmm27.ff in Gromacs). Users should not be led to believe that this tarball contains the full CHARMM36 force field, which is a different entity, available only from the MacKerell lab (note we will be uploading a new tarball soon that has updated parameters for CGenFF 2b8). -Justin -- 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.
Re: [gmx-users] errors with charmm36 ?
On 1/14/14, 11:38 AM, Albert wrote: It is good to know that the c36 and CGenFF is actively update. I just noticed that this new version c36 no longer contains classic TII3P water models: 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H 2: TIP4P TIP 4-point 3: TIP5P TIP 5-point 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None So in priciple, we have to use CHARMM TIP3P model, is it correct? You can use TIP3P without LJ terms on H atoms by making use of a define statement in the .mdp file; see ffnonbonded.itp for details. We promote the use of the TIP3P model with LJ on H because it makes a huge difference for some systems, especially lipids. Proteins are less sensitive to differences between the two TIP3P variants. But strictly speaking, with CHARMM, we always use the TIP3P model with LJ terms on H atoms since that's what we do during parametrization. I am always wondering, would it be better if there is a tool that could convert the output from paramchem websever into a single ligand.itp file? The parachem website can export the results including all known information from CGenFF related to target ligand. In such compelte output file, it contains all necessary information for a ligand parameters and toplogy We're working on that. Seamless integration between the different software packages is a goal we have. For now, you'll have to hack the output a bit to make it syntactically correct. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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.
Re: [gmx-users] errors with charmm36 ?
I would just like to also re-iterate the point made by Justin. The conversion of the lipid parameters into GROMACS format was done before there were published updates to other parts of the CHARMM force field and so it is only the lipids which are the CHARMM36 parameters. Regarding the choice of TIP3P water to use, further details regarding the impact of the water model upon lipid membranes (which can be large) and proteins (which was suggested to be minimal) can be seen in the following papers: Lipids: http://pubs.acs.org/doi/abs/10.1021/ct3003157 Proteins: http://pubs.acs.org/doi/abs/10.1021/ct900549r Cheers Tom Justin Lemkul wrote: On 1/14/14, 10:58 AM, hubert santuz wrote: I use this charmm36 (http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz, from Piggot et al, 2012, JCTC) which have slight differences in the order and in the name of few atoms compared to the one you used. So, everything I said concern only this version ;) I think it is probably worth emphasizing a point I have made previously, because I suspect there may be some confusion among the users out there. The tarball that can be downloaded from the website contains updated parameters for CHARMM36 lipids ONLY. The parameters in that distribution have outdated CHARMM22+CMAP parameters for proteins and CHARMM27 for nucleic acids (i.e. the files distributed as charmm27.ff in Gromacs). Users should not be led to believe that this tarball contains the full CHARMM36 force field, which is a different entity, available only from the MacKerell lab (note we will be uploading a new tarball soon that has updated parameters for CGenFF 2b8). -Justin Cheers, Hubert Le 14/01/2014 16:42, Albert a écrit : On 01/14/2014 04:12 PM, Justin Lemkul wrote: The .top is what matters, and your topology showed a clearly different order of atoms. Check the correspondence of the output configuration from pdb2gmx and the .top file. Inputs and .rtp entries are irrelevant once pdb2gmx is done working. -Justin Hi Justin: Many thanks for your helpful advices. The problem solved now. I some kind of mix the old c36 FF with the new one. I just update it in my system few days ago. thanks again for sugguestions. best Albert -- Dr Thomas Piggot University of Southampton, UK. -- 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.
