Quoting SWAPNA <[EMAIL PROTECTED]>: > Hi, > I am doing the Kerrigan Drug-enzyme tutorial. > I could generate the drg.itp, drg.gro files using PRODRG server. > When I use the grompp step before the energy minimization I encounter a > problem > -------------------------------- > A fatal error was shown: atom types CB, CR61 and OS were not found. > > ------------------------------- > These atom types CB, CR61 and OS are present in the drg.itp file. I > included the drg.itp file to the trp.top file before submission for > preprocesing using grompp. > > I have checked with atom types present in the forcefield files of my > gromacs version and found that these are not present in my force field > files.
If you are following the tutorial, you are using ffgmx, are you not? These atom types are indeed part of this force field. Have a look at ffgmx.atp and you will find all of them. I suspect an error within the topology, perhaps a typo in the include statement. -Justin > > What should I do to eliminate the error? > > Can you please give me the other corresponding atom types that may be > used for these unrecognised atom types? > > > > the drg.itp file that I used with the atom types CB, CR61 and OS > -------------------------------------------------------------------------- > ; > ; > ; This file was generated by PRODRG version 061128.0522 > ; PRODRG written/copyrighted by Daan van Aalten > ; and Alexander Schuettelkopf > ; > ; Questions/comments to [EMAIL PROTECTED] > ; > ; When using this software in a publication, cite: > ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). > ; PRODRG - a tool for high-throughput crystallography > ; of protein-ligand complexes. > ; Acta Crystallogr. D60, 1355--1363. > ; > ; > > [ moleculetype ] > ; Name nrexcl > IN4 3 > > [ atoms ] > ; nr type resnr resid atom cgnr charge mass > 1 NT 1 IN4 N3 1 0.144 14.0067 > 2 H 1 IN4 HAA 1 0.072 1.0080 > 3 H 1 IN4 HAB 1 0.072 1.0080 > 4 CB 1 IN4 C20 1 0.423 12.0110 > 5 NT 1 IN4 N4 1 0.145 14.0067 > 6 H 1 IN4 HAF 1 0.072 1.0080 > 7 H 1 IN4 HAE 1 0.072 1.0080 > 8 CB 1 IN4 C6 2 0.000 12.0110 > 9 CR61 1 IN4 C5 2 0.000 13.0190 > 10 CR61 1 IN4 C1 3 0.000 13.0190 > 11 CR61 1 IN4 C2 3 0.000 13.0190 > 12 CR61 1 IN4 C3 3 0.000 13.0190 > 13 CB 1 IN4 C4 3 0.000 12.0110 > 14 CH1 1 IN4 C10 3 0.000 13.0190 > 15 CH2 1 IN4 C14 4 0.131 14.0270 > 16 C 1 IN4 C22 4 0.469 12.0110 > 17 O 1 IN4 O3 4 -0.576 15.9994 > 18 OS 1 IN4 O4 4 -0.113 15.9994 > 19 CH3 1 IN4 C8 4 0.089 15.0350 > 20 CH2 1 IN4 C9 5 0.000 14.0270 > 21 CH2 1 IN4 C11 5 0.000 14.0270 > 22 CB 1 IN4 C12 5 0.000 12.0110 > 23 CR61 1 IN4 C19 5 0.000 13.0190 > 24 CR61 1 IN4 C17 5 0.000 13.0190 > 25 CR61 1 IN4 C7 6 0.000 13.0190 > 26 CR61 1 IN4 C13 6 0.000 13.0190 > 27 CB 1 IN4 C15 6 0.000 12.0110 > 28 CB 1 IN4 C16 7 0.423 12.0110 > 29 NT 1 IN4 N1 7 0.144 14.0067 > 30 H 1 IN4 HAH 7 0.072 1.0080 > 31 H 1 IN4 HAG 7 0.072 1.0080 > 32 NT 1 IN4 N2 7 0.145 14.0067 > 33 H 1 IN4 HAD 7 0.072 1.0080 > 34 H 1 IN4 HAC 7 0.072 1.0080 > > > Thanks!! > > Swapna > -- > The logic of life lies exclusively neither in the most incredible > detail, nor in the most sweeping synopsis. > _______________________________________________ > gmx-users mailing list [email protected] > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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
