Re[2]: 回复： [gmx-users] No such moleculetype Na

Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- 11年12月11日，周日, Setare Jiji jj.64fh...@yahoo.com 写道： 发件人: Setare Jiji jj.64fh...@yahoo.com 主题: [gmx-users] No such moleculetype

[gmx-users] No such moleculetype Na

Hi, Thanks for your responding. I checked my ions.itp file in which file sodium and chlorine ions are as Na and Cl form. Thus, I used genion as follows: genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn 8 -pname Na Unfortunately, I encountered same fatal error. any help

Re: [gmx-users] No such moleculetype Na

On 11/12/2011 8:17 PM, Setare Jiji wrote: Hi, Thanks for your responding. I checked my ions.itp file in which file sodium and chlorine ions are as Na and Cl form. Thus, I used genion as follows: genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -nname Cl -nn 8 -pname Na

回复： [gmx-users] No such moleculetype Na

Beichen West Road,Chaoyang District,Beijing 100101,china --- 11年12月11日，周日, Setare Jiji jj.64fh...@yahoo.com 写道： 发件人: Setare Jiji jj.64fh...@yahoo.com 主题: [gmx-users] No such moleculetype Na 收件人: gmx-users@gromacs.org 日期: 2011年12月11日,周日,下午5:17 Hi, Thanks for your responding. I checked

Re: 回复： [gmx-users] No such moleculetype Na

, Setare Jiji /jj.64fh...@yahoo.com/* 写道： 发件人: Setare Jiji jj.64fh...@yahoo.com 主题: [gmx-users] No such moleculetype Na 收件人: gmx-users@gromacs.org 日期: 2011年12月11日,周日,下午5:17 Hi, Thanks for your responding. I checked my ions.itp file in which file sodium and chlorine ions

Re: [gmx-users] No such moleculetype Na

Did you try NA or CL. All caps worked for me last time I used this. Egy On Dec 11, 2011, at 4:17 AM, Setare Jiji wrote: Hi, Thanks for your responding. I checked my ions.itp file in which file sodium and chlorine ions are as Na and Cl form. Thus, I used genion as follows: genion -s

[gmx-users] No such moleculetype Na

Hi, I am running Tutorial 1: Lysozyme in Water. I used 4-0-7 version and the sequence is true but in minimization energy step,I have this fatal error:   No such moleculetype Na so,what do I do? Best regards -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] No such moleculetype Na

Hi Setare, That tutorial is made for later gromacs versions, as stated at the beginning. The naming of ions has changed since 4.0.*. Cheers, Tsjerk On Dec 10, 2011 1:00 PM, Setare Jiji jj.64fh...@yahoo.com wrote: Hi, I am running Tutorial 1: Lysozyme in

Re: [gmx-users] No such moleculetype Na

Hi Setare, You should find the ions.itp file in your computer, open and see the exact name of sodium in this file. Use this name when using the command genion. Good luck! Cuong 2011/12/10 Setare Jiji jj.64fh...@yahoo.com Hi, I am running Tutorial 1: Lysozyme in

Re: [gmx-users] No such moleculetype NA+

with the issue.Any suggestions please. sree. -- Forwarded message -- From: shikha agarwal shikhaiiit...@gmail.com To: gmx-users@gromacs.org Date: Sun, 26 Dec 2010 12:26:16 +0530 Subject: [gmx-users] No such moleculetype NA+ hello , this is my ions.itp file for gromos53a6 forcefield

[gmx-users] No such moleculetype NA+

hello , this is my ions.itp file for gromos53a6 forcefield [ moleculetype ] ; molnamenrexcl CU11 [ atoms ] ; idat typeres nr residu nameat name cg nrcharge mass 1CU1+1CU1CU 11 63.54600 [ moleculetype ] ; molnamenrexcl CU

Re: [gmx-users] No such moleculetype NA+

Have a look at the rtp file of the force field u r using for correct representation of the ion used.. With regards, J. John Wesly, FInal Year, B.Tech., Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India. ~WesFaith~ He who desire to learn,

[gmx-users] No such moleculetype Na

Hi, I am performing the simulation of DNA in Gromacs using AMBER03 force field. The charge on the system is large (-23). I get grompp error when I add the relevant number of Na+ atoms. Program grompp_mpi, VERSION 3.3.1 Source code file: toppush.c, line: 1293 Fatal error: No such moleculetype Na

Re: [gmx-users] No such moleculetype Na

Hi Swati, Fatal error: No such moleculetype Na But the atom type is present in ffamber03.rtp. I tried changing the atom name to NA and Na+. But I still get similar error. Kindly help. It doesn't complain about the atom type, but about the moleculetype. Did you #include ions.itp? That file

Re: [gmx-users] No such moleculetype Na

Hi Tsjerk, Thanks for your reply. ions.itp is already included in topology file. However after you mentioned I checked the ions.itp file. But I think it defines molecule type only for gromacs force fields and the OPLS force field. The headers are only these three #ifdef _FF_GROMACS #ifdef

Re: [gmx-users] No such moleculetype Na

Hi Swati, Sorry, I wasn't paying that much attention indeed and failed to notice you were dealing with Amber. There's nothing wrong with your installation in this regard; Gromacs just does not have Amber included by default. I'm not sure if there's an ions.itp for Amber somewhere, but it's not

Re: [gmx-users] No such moleculetype Na

Hi Tsjerk, Thanks for your suggestion.I tried to change the ions.itp as follows : #ifdef _FF_AMBER03 [ moleculetype ] ; molname nrexcl Na+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 Na 1 Na Na 1 1

Re: [gmx-users] No such moleculetype Na

Hi Tsjerk, Thanks for your suggestions.After including molecule types from ions.itp for OPLS force field,its working fine now. Thanks again. Regards, Swati Hi Swati, Sorry, I wasn't paying that much attention indeed and failed to notice you were dealing with Amber. There's nothing wrong