Dear Dr. Tsjerk, Many many thanks for your help. This makes me some sense but still I am confused about that you indicated me to look out the gromacs/share directory. In my gromacs, I have following directory tree: gromacs/share/gromacs/top I did not found a format. I am wandering what could be that file in which I can check format. Other is, What I am doing my simulation is: pdb2gmx--->editconf.--->genbox---grompp---mdrun. But to get (.tpr) I need to pass editconf first. Would you please let me know how do I include mass on (.pdb). Thanks alot Hari
On Sunday, November 17, 2013 11:16 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: Hi Hari, The .pdb file you use as input has no masses listed. Editconf then resorts to a file called atommass.dat. You can check the format in the gromacs share directory and put a file in the same format in the working directory. Alternatively, you can make a run input file (.tpr) of your system and use that as input to editconf. The .tpr file has the real masses, taken from the atomtype definitions. Hope it helps, Tsjerk On Mon, Nov 18, 2013 at 4:46 AM, Hari Pandey <hariche...@yahoo.com> wrote: Dear Gromacs users: >I am hanging on the problems with editconf: can any one , please help me: >my problem is editconf displays wrong value of mass of input: >In Last post JUSTIN pointed out that he got correct value, while he run , but >let me post all about my problem: >My atomtypes.atp has only two atoms( I make it) >H 1.00800 >SOD 22.99 >My aminoacids.rtp has two rasidues >[ SOD ] > [ atoms ] > SOD SOD 1 1 >[ AIT ] > [ atoms ] > H1 H 1 0 >my aa.pdb has three atoms >ATOM 1 H1 AIT 1 14.328 -11.667 1.544 1.00 0.00 >ATOM 2 H2 AIT 1 15.013 -11.434 0.080 1.00 0.00 >ATOM 3 SOD SOD 2 5.599 4.582 0.028 1.00 0.00 >For testing purpose I used : pdb2gmx -f aa.pdb -o aaa.pdb and I have following: >ATOM 1 H1 AIT 1 14.328 -11.667 1.544 1.00 0.00 H >ATOM 2 H2 AIT 1 15.013 -11.434 0.080 1.00 0.00 H >ATOM 3 SOD SOD 2 5.599 4.582 0.028 1.00 0.00 S >Clearly Gromacs updating my SOD atom as S atom >When I do editconf ::: editconf -f aaa.pdb -o aa.gro -density 10000; it >showing following output with incorrect result. I did -density because I need >density of input for my research: > >WARNING: Masses and atomic (Van der Waals) radii will be guessed > based on residue and atom names, since they could not be > definitively assigned from the information in your input > files. These guessed numbers might deviate from the mass > and radius of the atom type. Please check the output > files if necessary. > >Volume of input 1.728 (nm^3) >Mass of input 34.0809 (a.m.u.) ( here we can see that gromacs is taking >sulphur atoms mass rather that mass os SOD >Density of input 32.7504 (g/l) >Scaling all box vectors by 0.319943 >new system size : 0.301 0.520 0.049 >new center : 0.373 -0.198 0.018 (nm) >new box vectors : 0.384 0.384 0.384 (nm) >new box angles : 90.00 90.00 90.00 (degrees) >new box volume : 0.06 (nm^3) > >I tried every possibilities. I updated name of atoms in all files , .pdb .atp >and .rtp everywhere. butt no benifit. SOMEBODY HELP ME PLEASE. What might be >its reason. Do I have to do something in source code or may be OS plateforms >any any possibility. PLEASE HELP ME. THIS ERROR IS HANGING ME SINCE A MONTH.If >I have to do something in source code please let me know which file should be >that. Or if it is due to environment then please let me know how do I come >over this problem.. >I tried alot. I rebooted my computer, I re installed gcc 4.8.2, Cmake latest, >git , FFTW3, all and finally gromacs 4.6.4 very recent release but still the >problem not gone away. Please help me > > > >Thanks in advance > > > > > > > > > > > > > > > > > > >On Sunday, November 17, 2013 3:01 AM, >"gromacs.org_gmx-users-requ...@maillist.sys.kth.se" ><gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > >Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > >To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > >You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of gromacs.org_gmx-users digest..." > > >Today's Topics: > > 1. Re: How to construct mixed lipid bilayer (Bj?rn Sommer) > (Bj?rn Sommer) > 2. Re: gromacs.org_gmx-users Digest, Vol 115, Issue 68 > (Raghunath Satpathy) > 3. Re: simulated annealing (Justin Lemkul) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Sat, 16 Nov 2013 23:29:40 +0100 >From: Bj?rn Sommer <bjo...@cellmicrocosmos.org> >To: gromacs.org_gmx-users@maillist.sys.kth.se >Subject: Re: [gmx-users] How to construct mixed lipid bilayer (Bj?rn > Sommer) >Message-ID: > <11315_1384640977_zzi0c2t2lmozm.00_5287f1d4.7030...@cellmicrocosmos.org> > >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >Am 13.11.2013 14:51, schrieb gmx-users-requ...@gromacs.org: >> Message: 4 >> Date: Wed, 13 Nov 2013 18:44:08 +0530 >> From: Nikhil Agrawal<nikhil.08...@gmail.com> >> Subject: [gmx-users] How to construct mixed lipid bilayer >> To:gmx-us...@gromacs.org >> Message-ID: >> <CAC4R+aJPnMFmn-RV=uggl+hnspaudyokyiijvkew0s22yrr...@mail.gmail.com> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Dear All, >> >> can anyone tell me how to construct mixed lipid bilayer in gromacs >> >> id possible also provide me the command to construct the mixed bilayer >> >> >> Thanks in advance >> >> Nikhil > >[Second try, my first mail seems to got lost due to mailing list migration] > >Dear Nikhil, > >especially for heterogeneous bilayers our MembraneEditor was developed, >you can download it here: > >http://Cm2.CELLmicrocosmos.org > >It is Java Webstart, so it is quite easy to use and install, but you can >also download the source code in the forum. > >Here you find some videos about how to use it: > >http://cellmicrocosmos.org/index.php/videos > >We also use it with Gromacs. There is no pre-euqilibration done in the >MembraneEditor. But we never needed it, because the equilibration with >Gromacs works very good. > >If you have further question, just let me know. A new version with a >number of improvements is coming during the next month! > >Best wishes, >Bj?rn > > >------------------------------ > >Message: 2 >Date: 17 Nov 2013 01:14:34 -0000 >From: "Raghunath Satpathy" <satpat...@rediffmail.com> >To: <gromacs.org_gmx-users@maillist.sys.kth.se> >Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue > 68 >Message-ID: > ><1384599990.S.7323.1575.H.Tmdyb21hY3Mub3JnX2dteC11c2Vycy1yZXF1ZXN0QABncm9tYWNzLm9yZ19nbXgtdXNlcnMgRGlnZXN0LCA_.RU.rfs278, > > rfs278, 649, > 412.f5-224-140.old.1384650874.21...@webmail.rediffmail.com> >Content-Type: text/plain; charset="UTF-8" > > > >is it necessary to heat and cool protein in simulated annealing ? i wanna to >check thermostability by md simulation only by increasing temp (without >cooling ) in many picoseconds , is it possible to get good result ? pls reply >soon > >------------------------------ > >Message: 3 >Date: Sat, 16 Nov 2013 20:31:15 -0500 >From: Justin Lemkul <jalem...@vt.edu> >To: Discussion list for GROMACS users > <gromacs.org_gmx-users@maillist.sys.kth.se> >Subject: Re: [gmx-users] simulated annealing >Message-ID: <52881c63.6000...@vt.edu> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > >Please use a descriptive subject line. > >On 11/16/13 8:14 PM, Raghunath Satpathy wrote: >> >> >> is it necessary to heat and cool protein in simulated annealing ? i wanna to >> check thermostability by md simulation only by increasing temp (without >> cooling ) in many picoseconds , is it possible to get good result ? pls >> reply soon >> > >What is "necessary" depends on what you are trying to achieve. See what others >do in the literature and develop a protocol based on what seems sensible. For >thermostability assessments, I don't see any immediate need to cycle >temperatures up and down. Simple heating could be perfectly reasonable. > >-Justin > >-- >================================================== > >Justin A. Lemkul, Ph.D. >Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 601 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >================================================== > > >------------------------------ > >-- >gromacs.org_gmx-users mailing list >gromacs.org_gmx-users@maillist.sys.kth.se >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >End of gromacs.org_gmx-users Digest, Vol 115, Issue 69 >****************************************************** >-- >gromacs.org_gmx-users mailing list gromacs.org_gmx-users@maillist.sys.kth.se >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >* Please don't post (un)subscribe requests to the list. Use the >www interface or send it to gmx-users-requ...@gromacs.org. >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- 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.
