Dear All, Can anyone help me in running simulation in explicit urea. When i was using urea+h2o.gro and urea.itp and tried to do simulation in explicit urea. After doing genbox, i am not able to do the grompp for energy minimization and getting the error which is given below.
I have added masses of all the atoms of urea in atommass.dat file, but still getting the same error. Please help me, where does am i making the mistakes. processing coordinates... Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) (more than 20 non-matching atom names) WARNING 3 [file "base.top", line 808]: 6150 non-matching atom names atom names from base.top will be used atom names from after_sol.gro will be ignored double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... # BONDS: 945 # G96BONDS: 128 # ANGLES: 1215 # G96ANGLES: 190 # PDIHS: 1134 # IDIHS: 485 # LJ14: 1242 # SETTLE: 2050 ERROR 4 [file "base.top", line 808]: atom C1 (Res UREA-11) has mass 0 ERROR 5 [file "base.top", line 808]: atom O2 (Res UREA-11) has mass 0 ERROR 6 [file "base.top", line 808]: atom N3 (Res UREA-11) has mass 0 ERROR 7 [file "base.top", line 808]: atom H4 (Res UREA-11) has mass 0 ERROR 8 [file "base.top", line 808]: atom H5 (Res UREA-11) has mass 0 ERROR 9 [file "base.top", line 808]: atom N6 (Res UREA-11) has mass 0 ERROR 10 [file "base.top", line 808]: atom H7 (Res UREA-11) has mass 0 ------------------------------------------------------- Program grompp, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated ------------------------------------------------------- "I'm An Oakman" (Pulp Fiction) Thanks in advance. With Warm Regards anil -- (¨`.´¨) Always `.¸(¨`.´¨) Keep (¨`.´¨)¸.´ Smiling! `.¸.´ «´`.(*.¸(`.¸ ¸.´)¸.*).´`» «´¨*.¸¸. * ANIL *.¸¸.*¨`» «´`.(¸.´(¸.* *.¸)`.¸).´`» ANIL KUMAR(Research Scholar), Bio-Organic Lab No-336(2nd Floor), Dept. of Chemistry,I.I.T.Bombay,Powai, Mumbai-400076, Ph. No.-022-25764780(Lab) ----------------------------------------- Residence:- Hostel#1,Room#297,IIT Bombay,Powai, Mumbai-400076,Ph.No.:-022-25721017(Hostel) ------------------------------------------------- Web:http://chemanil.googlepages.com/ -------------------------- "Education is a progressive discovery of our ignorance" - Will Durant ---------------------------- > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: CNT Potassium doping with GROMACS (George Abadir) > 2. Re: Cannot find fftw3f (Mark Abraham) > 3. Re: suggest small revision to genbox (bharat v. adkar) > 4. Re: suggest small revision to genbox (David van der Spoel) > 5. Error while running MD in DMSO! (Anil Kumar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 May 2007 18:52:43 -0700 > From: George Abadir <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] CNT Potassium doping with GROMACS > To: [EMAIL PROTECTED], Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Another point: is it possible to use pdb2gmx to do the job instead of > x2top? I tried and used the GROMOS96 43b1 vacuum force field (since the > doping by potassium is in vacuum), but i got the error"Residue 'CNT' not > found in residue topolgy database'. I went to the 'ffg43b1.rtp' file in > the /share/top folder and defined it as '[CNT] > > > [atoms] > > > C C 0 0' > but still get the same error. > Your help is much appreciated, > Thank you in advance, > George > > George Abadir wrote: > >> Hi, >> I want to make a simulation of CNT in an environment of potassium >> atoms to see how they will be adsorbed on the CNT surface (this is a >> way of doping carbon nanotubes). I built a .pdb file with a CNT and >> some potassium atoms with random coordinates around the nanotube. When >> I run x2top to have my topology file, I get the error:"No forcefield >> type for atom K with 0 bond". The problem is that the atoms of >> potassium should indeed be not bonded to anything at the beginning of >> the simulation. Does anybody have a way to describe such a system and >> avoid this error? >> Thank you very much in advance, >> Regards, >> George >> _______________________________________________ >> gmx-users mailing list gmx-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 >> >> > > > > ------------------------------ > > Message: 2 > Date: Sat, 12 May 2007 12:22:41 +1000 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Cannot find fftw3f > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Omovie, Sheyore John wrote: >> Hi, >> Even after following the instructions in the HowTo Cygwin and gromacs, I >> still come up >> with the configure error:Cannot find fftw3f. > > The most likely thing is that you haven't actually followed the > instructions precisely... > http://www.gromacs.org/pipermail/gmx-users/2006-April/021147.html In > particular you need "--enable-float" with configure for fftw. > >> I ahve also tried specifying the header file directory, it still doesn't >> work. > > No, that wouldn't help. > >> I would appreciate any advice on overcoming this problem. > > In the absence of more information from you, all I can suggest is trying > again :-) In extremis, re-installing cygwin has helped another user. > > Mark > > > ------------------------------ > > Message: 3 > Date: Sat, 12 May 2007 12:05:44 +0530 (IST) > From: "bharat v. adkar" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] suggest small revision to genbox > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > genbox works fine for me. i use 3.3.1 version. it works fine with and > without script. > > but i don't understand how will u get rid of backup files in the permanent > directory from whatever u have mentioned, because gromacs creates the > output topology in the same location where it reads the input topology > from. so temperory directory thing will work only if u make an link of top > file from permanent directory and use this linked version as input, then > move the new top from temp to permanent directory. > > bharat > > > > > > On Fri, 11 May 2007, David Mobley wrote: > >> All, >> >> I'm trying to write some wrappers to set up a project using standard >> gromacs tools. Anyway, it looks to me like genbox is not handling its >> path names correctly. In particular, here's what I did: >> >> - Make temporary directory in which to run genbox >> - Move to temporary directory, run genbox (reading input files from >> permanent directory; writing input files to permanent directory) >> - Change back to starting directory; delete temporary directory >> >> When I do this, I get a blank output topology file in my permanent >> directory. >> >> It appears what's going on is that the file temp.top is written into >> my temporary directory, but never moved into the permanent directory; >> I suspect genbox is not handling the absolute/relative path issue >> correctly here? >> >> I can work around, but this is just a bit annoying -- when I script >> it, I end up with a bunch of "#temp.top.1#" etc files in my working >> directory if I use editconf in the normal way, which is why I was >> using the temporary directory thing to begin with. >> >> Thanks, >> David >> _______________________________________________ >> gmx-users mailing list gmx-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 >> >> > > > ------------------------------ > > Message: 4 > Date: Sat, 12 May 2007 11:13:00 +0200 > From: David van der Spoel <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] suggest small revision to genbox > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > David Mobley wrote: >> All, >> >> I'm trying to write some wrappers to set up a project using standard >> gromacs tools. Anyway, it looks to me like genbox is not handling its >> path names correctly. In particular, here's what I did: >> >> - Make temporary directory in which to run genbox >> - Move to temporary directory, run genbox (reading input files from >> permanent directory; writing input files to permanent directory) >> - Change back to starting directory; delete temporary directory >> >> When I do this, I get a blank output topology file in my permanent >> directory. >> >> It appears what's going on is that the file temp.top is written into >> my temporary directory, but never moved into the permanent directory; >> I suspect genbox is not handling the absolute/relative path issue >> correctly here? >> >> I can work around, but this is just a bit annoying -- when I script >> it, I end up with a bunch of "#temp.top.1#" etc files in my working >> directory if I use editconf in the normal way, which is why I was >> using the temporary directory thing to begin with. >> > Hi David, > > plz submit a bugzilla with all input and scripts. > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > ------------------------------ > > Message: 5 > Date: Sat, 12 May 2007 14:03:11 +0530 (IST) > From: "Anil Kumar" <[EMAIL PROTECTED]> > Subject: [gmx-users] Error while running MD in DMSO! > To: [EMAIL PROTECTED], gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain;charset=iso-8859-1 > > Dear All, > > I am running my simulations in explicit MeOH and DMSO. In case of MeOH, it > is running fine but while running in DMSO. > > After running genbox i am having problem in running grompp for energy > minimization. > Error which i got is given below. > > Cleaning up temporary file gromppkkHvWC > Fatal error: Atomtype 'SD' not found! > > Please, anyone let me know why it is happening when i had used the > dmso.gro and dmso.itp files which is available by default to top folder. > > Thanks in advance. > > With Warm Regards > Anil > > -- > (¨`.´¨) Always > `.¸(¨`.´¨) Keep > (¨`.´¨)¸.´ Smiling! > `.¸.´ > «´`.(*.¸(`.¸ ¸.´)¸.*).´`» > «´¨*.¸¸. * ANIL *.¸¸.*¨`» > «´`.(¸.´(¸.* *.¸)`.¸).´`» > > ANIL KUMAR(Research Scholar), > Bio-Organic Lab No-336(2nd Floor), > Dept. of Chemistry,I.I.T.Bombay,Powai, > Mumbai-400076, > Ph. No.-022-25764780(Lab) > ----------------------------------------- > Residence:- > Hostel#1,Room#297,IIT Bombay,Powai, > Mumbai-400076,Ph.No.:-022-25721017(Hostel) > ------------------------------------------------- > Web:http://chemanil.googlepages.com/ > -------------------------- > "Education is a progressive discovery of our ignorance" > > - Will Durant > ---------------------------- > > > > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 37, Issue 44 > ***************************************** > _______________________________________________ gmx-users mailing list gmx-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