[gmx-users] About the example case A toy peptide in water and other protein case (CG martini force field )
Dear Sir , I used your CG parameters and gromacs V3.3 to simulate protein aggregation. And my command is : grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp The error message is : double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # BONDS: 1935 # G96ANGLES: 2565 # IDIHS: 225 # CONSTR: 900 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /opt/gromacs//share/gromacs/top/aminoacids.dat There are: 76048 OTHER residues There are: 1170 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group Protein1 not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. But I tried your example case A toy peptide in water , I still got the same error . My command is : 1.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -n index.ndx -o toypeptide.tpr 2.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -o toypeptide.tpr index.ndx : [ prot_sort ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 The error message : Walking down the molecule graph to make shake-blocks initialising group options... processing index file... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group TOYPEP not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Sir, could you tell me how to fix the problem? By the way, I test other cases in your website and I didn't get any error message . Best regards Wang Yeng-tseng begin:vcard fn:Yeng-Tseng Wang n:Wang;Yeng-Tseng org;quoted-printable;quoted-printable:=E7=94=9F=E6=8A=80=E9=86=AB=E7=99=82=E8=B3=87=E8=A8=8A=E7=B5=84;=E5=8D=97=E9=83=A8=E4=BA=8B=E6=A5=AD=E7=BE=A4 adr;quoted-printable;quoted-printable;quoted-printable;quoted-printable:;;=E5=8F=B0=E5=8D=97=E7=B8=A3=E6=96=B0=E5=B8=82=E9=84=89=E5=8D=97=E7=A7=91=E4= =B8=89=E8=B7=AF28=E8=99=9F;=E5=8F=B0=E5=8D=97=E7=B8=A3;=E6=96=B0=E5=B8=82=E9=84=89;74114;=E4=B8=AD=E8=8F=AF=E6=B0=91=E5=9C=8B(=E5=8F=B0=E7=81=A3) email;internet:[EMAIL PROTECTED] title;quoted-printable:=E8=B2=A1=E5=9C=98=E6=B3=95=E4=BA=BA=E5=9C=8B=E5=AE=B6=E5=AF=A6=E9=A9=97=E7= =A0=94=E7=A9=B6=E9=99=A2=E5=9C=8B=E5=AE=B6=E9=AB=98=E9=80=9F=E7=B6=B2=E8=B7= =AF=E8=88=87=E8=A8=88=E7=AE=97=E4=B8=AD=E5=BF=83 tel;work:+886-5050940 ext.738 tel;cell:+886-939875770 url:http://www.nchc.org.tw version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] About the example case A toy peptide in water and other protein case (CG martini force field )
Dear Sir , I used your CG parameters and gromacs V3.3 to simulate protein aggregation. And my command is : grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp The error message is : double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # BONDS: 1935 # G96ANGLES: 2565 # IDIHS: 225 # CONSTR: 900 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /opt/gromacs//share/gromacs/top/aminoacids.dat There are: 76048 OTHER residues There are: 1170 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group Protein1 not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. But I tried your example case A toy peptide in water , I still got the same error . My command is : 1.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -n index.ndx -o toypeptide.tpr 2.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -o toypeptide.tpr index.ndx : [ prot_sort ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 The error message : Walking down the molecule graph to make shake-blocks initialising group options... processing index file... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group TOYPEP not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Sir, could you tell me how to fix the problem? By the way, I test other cases in your website and I didn't get any error message . Best regards Wang Yeng-tseng begin:vcard fn:Yeng-Tseng Wang n:Wang;Yeng-Tseng org;quoted-printable;quoted-printable:=E7=94=9F=E6=8A=80=E9=86=AB=E7=99=82=E8=B3=87=E8=A8=8A=E7=B5=84;=E5=8D=97=E9=83=A8=E4=BA=8B=E6=A5=AD=E7=BE=A4 adr;quoted-printable;quoted-printable;quoted-printable;quoted-printable:;;=E5=8F=B0=E5=8D=97=E7=B8=A3=E6=96=B0=E5=B8=82=E9=84=89=E5=8D=97=E7=A7=91=E4= =B8=89=E8=B7=AF28=E8=99=9F;=E5=8F=B0=E5=8D=97=E7=B8=A3;=E6=96=B0=E5=B8=82=E9=84=89;74114;=E4=B8=AD=E8=8F=AF=E6=B0=91=E5=9C=8B(=E5=8F=B0=E7=81=A3) email;internet:[EMAIL PROTECTED] title;quoted-printable:=E8=B2=A1=E5=9C=98=E6=B3=95=E4=BA=BA=E5=9C=8B=E5=AE=B6=E5=AF=A6=E9=A9=97=E7= =A0=94=E7=A9=B6=E9=99=A2=E5=9C=8B=E5=AE=B6=E9=AB=98=E9=80=9F=E7=B6=B2=E8=B7= =AF=E8=88=87=E8=A8=88=E7=AE=97=E4=B8=AD=E5=BF=83 tel;work:+886-5050940 ext.738 tel;cell:+886-939875770 url:http://www.nchc.org.tw version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] About the example case A toy peptide in water and other protein case (CG martini force field )
Dear Sir , I used your CG parameters and gromacs V3.3 to simulate protein aggregation. And my command is : grompp_mpi_d -np 2 -f aggre.mdp -c aggre.gro -p aggre.top -o aggre.trp The error message is : double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... # BONDS: 1935 # G96ANGLES: 2565 # IDIHS: 225 # CONSTR: 900 Walking down the molecule graph to make shake-blocks initialising group options... processing index file... Analysing residue names: Opening library file /opt/gromacs//share/gromacs/top/aminoacids.dat There are: 76048 OTHER residues There are: 1170 PROTEIN residues There are: 0 DNA residues Analysing Protein... Analysing Other... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group Protein1 not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. But I tried your example case A toy peptide in water , I still got the same error . My command is : 1.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -n index.ndx -o toypeptide.tpr 2.grompp_mpi_d -np 2 -f toypeptide.mdp -p toypeptide.top -c toypeptide.gro -o toypeptide.tpr index.ndx : [ prot_sort ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 The error message : Walking down the molecule graph to make shake-blocks initialising group options... processing index file... --- Program grompp_mpi_d, VERSION 3.3.3 Source code file: readir.c, line: 798 Fatal error: Group TOYPEP not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. Sir, could you tell me how to fix the problem? By the way, I test other cases in your website and I didn't get any error message . Best regards Wang Yeng-tseng begin:vcard fn:Yeng-Tseng Wang n:Wang;Yeng-Tseng org;quoted-printable;quoted-printable:=E7=94=9F=E6=8A=80=E9=86=AB=E7=99=82=E8=B3=87=E8=A8=8A=E7=B5=84;=E5=8D=97=E9=83=A8=E4=BA=8B=E6=A5=AD=E7=BE=A4 adr;quoted-printable;quoted-printable;quoted-printable;quoted-printable:;;=E5=8F=B0=E5=8D=97=E7=B8=A3=E6=96=B0=E5=B8=82=E9=84=89=E5=8D=97=E7=A7=91=E4= =B8=89=E8=B7=AF28=E8=99=9F;=E5=8F=B0=E5=8D=97=E7=B8=A3;=E6=96=B0=E5=B8=82=E9=84=89;74114;=E4=B8=AD=E8=8F=AF=E6=B0=91=E5=9C=8B(=E5=8F=B0=E7=81=A3) email;internet:[EMAIL PROTECTED] title;quoted-printable:=E8=B2=A1=E5=9C=98=E6=B3=95=E4=BA=BA=E5=9C=8B=E5=AE=B6=E5=AF=A6=E9=A9=97=E7= =A0=94=E7=A9=B6=E9=99=A2=E5=9C=8B=E5=AE=B6=E9=AB=98=E9=80=9F=E7=B6=B2=E8=B7= =AF=E8=88=87=E8=A8=88=E7=AE=97=E4=B8=AD=E5=BF=83 tel;work:+886-5050940 ext.738 tel;cell:+886-939875770 url:http://www.nchc.org.tw version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
