Re: [gmx-users] grompp erro
Here are the atoms mentioned in the log file: 1NH2 19THR N 1 -0.96 14.007 ; qtot -0.96 3CT1 19THR CA 4 0.19 12.011 ; qtot -0.09 4CT1 19THR CB 6 0.14 12.011 ; qtot 0.14 5HB1 19THR HA 5 0.09 1.008 ; qtot 0 On 01/19/2014 09:46 PM, Justin Lemkul wrote: OK, now please provide the rest of the information I asked for in my other email: What are those atoms and what are their types? Only you know what your topology is. Please make it easy and expedient to help us to help you! -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] grompp erro
On 01/19/2014 06:07 PM, Justin Lemkul wrote: That still doesn't provide anything more useful than before. Please answer the questions I posed in my last message. The essential information is on line 23560 of the problematic topology. -Justin Here is the line: [ angles ] ; aiajak functc0c1 c2c3 2 1 3 5 2 1 4 5 3 1 4 5 (---line 23560) -- 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.
[gmx-users] amidation at Met
Hello: I've got an amidation at a c terminal Met residue. I am just wondering is there any parameter in latest c36 FF for such kind of residue? thank you very much. 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.
[gmx-users] -norandom option removed?
Hello: I found that the -norandom option in genion was no longer in 4.6.5: genion -h Option Filename Type Description -s topol.tpr InputRun input file: tpr tpb tpa -n index.ndx Input, Opt. Index file -oout.gro Output Structure file: gro g96 pdb etc. -p topol.top In/Out, Opt. Topology file Option Type Value Description -- -[no]h bool yes Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -np int0 Number of positive ions -pname string NA Name of the positive ion -pq int1 Charge of the positive ion -nn int0 Number of negative ions -nname string CL Name of the negative ion -nq int-1 Charge of the negative ion -rminreal 0.6 Minimum distance between ions -seedint1993Seed for random number generator -concreal 0 Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input .tpr file. Overrides the -np and -nn options. -[no]neutral bool no This option will add enough ions to neutralize the system. These ions are added on top of those specified with -np/-nn or -conc. I am just wondering does it means the pme methods would be automatically for ion placement? thank you very much. 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 ?
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 ?
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.
