Re: [gmx-users] TOPOLOGY AND GRO FILE ATOMS NAME MISMATCH
Hi I believe gromacs uses atom names from topology if they are not matching. Check atoms in PDB and compare them with topology then you will find what is missing or the differences Ali On Sun, Nov 4, 2018 at 7:05 AM K. Subashini wrote: > Hi gromacs users, > > For an organic molecule, the topology file was built using opls > forcefield was obtained. > > Using gmx insert command, the gro file containing 150 molecules of the > same organic compound placed in a box was obtained. > > Now the topology and gro file have non-matching atom names. > > > How to fix the error? > > Thanks, > Subashini.K > > -- > 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. > -- 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] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug
Hi again, additional info about my issue with DensMap and xpm2ps I noticed that the number of decimals of the x/y axis values in the xpm are smaller may have an effect of presence of the minor and major ticks in eps file obtained from xpm2ps (see below) Indeed with the same following params in the m2p x-major = 1.0 x-minor = 0.1 x-firstmajor = 0.0 y-major = 1.0 y-minor = 0.1 y-firstmajor = 0.0 and different examples 1) With PDB as input and 1 frame I obtained the following xpm with the x-values (only a small part is shown) ---> minor and major ticlks are present in the eps /* x-axis: 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1 1.05 1.1 1.15 1.2 1.25 1.3 1.35 1.4 1.45 1.5 1.55 1.6 1.65 1.7 1.75 1.8 1.85 1.9 1.95 2 2.05 2.1 2.15 2.2 2.25 2.3 2.35 2.4 2.45 2.5 2.55 2.6 2.65 2.7 2.75 2.8 2.85 2.9 2.95 3 3.05 3.1 3.15 3.2 3.25 3.3 3.35 3.4 3.45 3.5 3.55 3.6 3.65 3.7 3.75 3.8 3.85 3.9 3.95 */ 2) With PDB as input and 1000 frame I obtained the following xpm with the x-values (only a small part is shown) ---> minor and major ticlks are NOT present in the eps /* x-axis: 0 0.0499876 0.0999751 0.149963 0.19995 0.249938 0.299925 0.349913 0.399901 0.449888 0.499876 0.549863 0.599851 0.649838 0.699826 0.749814 0.799801 0.849789 0.899776 0.949764 0.999751 1.04974 1.09973 1.14971 1.1997 1.24969 1.29968 1.34966 1.39965 1.44964 1.49963 1.54961 1.5996 1.64959 1.69958 1.74957 1.79955 1.84954 1.89953 1.94952 1.9995 2.04949 2.09948 2.14947 2.19945 2.24944 2.29943 2.34942 2.3994 2.44939 2.49938 2.54937 2.59935 2.64934 2.69933 2.74932 2.7993 2.84929 2.89928 2.94927 2.99925 3.04924 3.09923 3.14922 3.1992 3.24919 3.29918 3.34917 3.39915 3.44914 3.49913 3.54912 3.59911 3.64909 3.69908 3.74907 3.79906 3.84904 3.89903 3.94902 */ 3) With XTC as input and 1 frame I obtained the following xpm with the x-values (only a small part is shown) ---> minor and major ticlks are NOT present in the eps /* x-axis: 0 0.054 0.11 0.150001 0.21 0.250002 0.32 0.350003 0.43 0.450003 0.54 0.550004 0.64 0.650005 0.75 0.750005 0.86 0.850006 0.97 0.950007 1.1 1.05001 1.10001 1.15001 1.20001 1.25001 1.30001 1.35001 1.40001 1.45001 1.50001 1.55001 1.60001 1.65001 1.70001 1.75001 1.80001 1.85001 1.90001 1.95001 2.1 2.05002 2.10002 2.15002 2.20002 2.25002 2.30002 2.35002 2.40002 2.45002 2.50002 2.55002 2.60002 2.65002 2.70002 2.75002 2.80002 2.85002 2.90002 2.95002 3.2 3.05002 3.10002 3.15002 3.20002 3.25002 3.30002 3.35002 3.40002 3.45003 3.50003 3.55003 3.60003 3.65003 3.70003 3.75003 3.80003 3.85003 3.90003 3.95003 */ and 4) With XTC as input and 1000 frames I obtained the following xpm with the x-values (only a small part is shown) ---> minor and major ticlks are NOT present in the eps /* x-axis: 0 0.0499876 0.0999751 0.149963 0.19995 0.249938 0.299925 0.349913 0.399901 0.449888 0.499876 0.549863 0.599851 0.649838 0.699826 0.749814 0.799801 0.849789 0.899776 0.949764 0.999751 1.04974 1.09973 1.14971 1.1997 1.24969 1.29968 1.34966 1.39965 1.44964 1.49963 1.54961 1.5996 1.64959 1.69958 1.74956 1.79955 1.84954 1.89953 1.94952 1.9995 2.04949 2.09948 2.14947 2.19945 2.24944 2.29943 2.34942 2.3994 2.44939 2.49938 2.54937 2.59935 2.64934 2.69933 2.74932 2.7993 2.84929 2.89928 2.94927 2.99925 3.04924 3.09923 3.14922 3.1992 3.24919 3.29918 3.34917 3.39915 3.44914 3.49913 3.54912 3.5991 3.64909 3.69908 3.74907 3.79906 3.84904 3.89903 3.94902 */ I used for the above examples the same densmap and xpm2ps commands show below and the 5.1.4 and 2018.2 gromacs version. It is a bug related to the rounding in the xpm2ps or I miss something ? Thank you in advance for your help Stéphane -- Message: 4 Date: Sat, 3 Nov 2018 17:45:53 + From: ABEL Stephane To: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: [gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap Message-ID: <3e39b768bb199548ab18f7289e7534af4887a...@exdag0-b0.intra.cea.fr> Content-Type: text/plain; charset="iso-8859-2" Thanks you Justin for your help but I still have the smae problem . I have changed in my m2p file the floowing fields x-major = 1.0; Major ticks on x axis every .. frames x-minor = 0.05 ; Id. Minor ticks x-firstmajor = 0.0 ; First frame for major tick y-major = 1.0 ; Major ticks on y axis every .. frames y-minor = 0.05 ; Id. Minor ticks y-firstmajor = 0.0 and use the xpm, some (not all) sticks appeared in each axis but w/o the labels. I still do not understand why ... St?phane -- On 11/3/18 12:19 PM, ABEL Stephane wrote: > Hello, > > I am using the below .m2p file as input
[gmx-users] TOPOLOGY AND GRO FILE ATOMS NAME MISMATCH
Hi gromacs users, For an organic molecule, the topology file was built using opls forcefield was obtained. Using gmx insert command, the gro file containing 150 molecules of the same organic compound placed in a box was obtained. Now the topology and gro file have non-matching atom names. How to fix the error? Thanks, Subashini.K -- 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.
