Re: [gmx-users] Error: Atomtype CH2 not found
If the itp is correct then modify atomnames2types to add the correct bonds and bond lengths PB > On Dec 13, 2019, at 7:52 PM, Justin Lemkul wrote: > > > >> On 12/13/19 2:18 AM, Muthusankar wrote: >> Dear Gromacs users, >> I am simulating a protein-ligand complex and performing the grompp command >> before adding ions to the system. I got the error. >> *Fatal error: *(file: ligand.itp) >> Atomtype *CH2 not found*. >> *command used:* >> gmx grompp -f ions.mdp -c protein_box.gro -p protein.top -o ions.tpr >> >> Please guide me, How to rectify the problem. >> > > This means you're trying to use an atom type that your force field doesn't > recognize. Either you're mixing and matching force fields (never do this) or > your ligand topology relies on new atom types that should be introduced into > the force field, in which case the source of the ligand topology (server, > etc.) should provide that information. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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.
Re: [gmx-users] Problem with GROMAC 2019.4
Great! What magic did you conjure up? PB > On Dec 13, 2019, at 12:56 PM, Avi Hundal wrote: > > Hi Paul, > > Yes sir, I am up and running. Thank you all! > > Regards, > > Avneel S. Hundal > > Email: havn...@gmail.com > > >> On Sun, Dec 8, 2019 at 3:48 AM Paul Buscemi wrote: >> >> Are you up And running? >> >> PB >> >>> On Dec 8, 2019, at 12:46 AM, Avi Hundal wrote: >>> >>> Hey Paul, >>> >>> Thanks for looking out. I found that out the hard way, I have gcc 8.0 >>> installed and configured it with '-config gcc'. >>> >>> Regards, >>> >>> Avneel S. Hundal >>> >>> Email: havn...@gmail.com >>> >>> On Sat, Dec 7, 2019 at 6:39 PM Paul Buscemi wrote: A shot in the dark. Cuda may not work with latest version of gcc. There >> is lit on this issue Try the repository version for cuda toolbox PB > On Dec 4, 2019, at 4:25 AM, Christian Blau wrote: -- 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] rotacf error
Hi all I want to calculate the order parameter of the NH vector for each amino acids of a protein in a gromacs trajectory for compare with NMR experimental data. I found that it can be calculated using rotacf to calculate the correlation time, when trying to run the program I get an error. In the attached file I show more details about the error andhow I created the index. Could you help me to correct the index for calculate the correlation time and in turn the order parameter S2? Thanks for your help. -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* gmx_mpi make_ndx -f protein_md.tpr -o nh.ndx << EOF > a N | a H > r 590 | r 645 | r 649 | r 655 | r 664 | r 680 > 10 & !11 > name 12 NH > del 0-11 > q > EOF > name 12 NH > del 0-11 > q > EOF Reading structure file Reading file cbd212_md.tpr, VERSION 2018.6 (single precision) Reading file cbd212_md.tpr, VERSION 2018.6 (single precision) Going to read 0 old index file(s) Analysing residue names: There are: 146Protein residues There are: 23993 Water residues There are: 196Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 74517 atoms 1 Protein : 2342 atoms 2 Protein-H : 1186 atoms 3 C-alpha : 146 atoms 4 Backbone: 438 atoms 5 MainChain : 585 atoms 6 MainChain+Cb: 723 atoms 7 MainChain+H : 727 atoms 8 SideChain : 1615 atoms 9 SideChain-H : 601 atoms 10 Prot-Masses : 2342 atoms 11 non-Protein : 72175 atoms 12 Water : 71979 atoms 13 SOL : 71979 atoms 14 non-Water : 2538 atoms 15 Ion : 196 atoms 16 NA : 103 atoms 17 CL :93 atoms 18 Water_and_ions : 72175 atoms nr : group '!': not 'name' nr name 'splitch' nrEnter: list groups 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 't': atom type '|': or 'keep' nr'splitat' nr'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index > Found 146 atoms with name N Found 139 atoms with name H Merged two groups with OR: 146 139 -> 285 19 N_H : 285 atoms > Merged two groups with OR: 14 14 -> 28 Merged two groups with OR: 28 14 -> 42 Merged two groups with OR: 42 14 -> 56 Merged two groups with OR: 56 14 -> 70 Merged two groups with OR: 70 14 -> 84 20 r_590_r_645_r_649_r_655_r_664_r_680:84 atoms > Copied index group 10 'Prot-Masses' Copied index group 11 'non-Protein' Complemented group: 2342 atoms Merged two groups with AND: 2342 2342 -> 2342 21 Prot-Masses_&_!non-Protein: 2342 atoms > > Removed group 0 'System' Removed group 1 'Protein' Removed group 2 'Protein-H' Removed group 3 'C-alpha' Removed group 4 'Backbone' Removed group 5 'MainChain' Removed group 6 'MainChain+Cb' Removed group 7 'MainChain+H' Removed group 8 'SideChain' Removed group 9 'SideChain-H' Removed group 10 'Prot-Masses' Removed group 11 'non-Protein' > gmx_mpi rotacf -s protein_md.tpr -f protein_nopbc.xtc -P 2 -d -n nh.ndx -o protein_rotacf.xvg -dt 1000 Group 0 ( NH) has 71979 elements Group 1 (SOL) has 71979 elements Group 2 ( non-Water) has 2538 elements Group 3 (Ion) has 196 elements Group 4 ( NA) has 103 elements Group 5 ( CL) has93 elements Group 6 ( Water_and_ions) has 72175 elements Group 7 (N_H) has 285 elements Group 8 (r_590_r_645_r_649_r_655_r_664_r_680) has84 elements Group 9 (Prot-Masses_&_!non-Protein) has 2342 elements Select a group: 7 Selected 7: 'N_H' --- Program: gmx rotacf, version 2018.6 Source file: src/gromacs/gmxana/gmx_rotacf.cpp (line 140) Fatal error: number of index elements not multiple of 2, these can not be atom doublets For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. -- 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-u
