Re: [gmx-users] OPLS modification between 3.3 and 3.3.1??
Hi Chris, This change was committed before we had started bugzilla, so thus no entry, but you can find it in the CVS log :-) It was covered on the mailing list, though. The torsion only affects non-standard protonation states of side chains that are not present in any OPLS-AA publication. The old version used the standard values (i.e., not OPLS-AA/L) while the newer ones just copy the OPLS-AA/L value. I really have no idea which one is better - the proper solution is for somebody to reparametrize it. In any case you will never get those residues unless you specify the protonation state manually. The charge distribution in MET has been modified to agree with later OPLS-AA/L values (instead of the 2000 ones). Cheers, Erik On Apr 19, 2006, at 9:41 PM, [EMAIL PROTECTED] wrote: Hello, ffoplsaa.rtp has changed in the 3.3.1 release. However, there are no references given and no special notification of this fact. I was wondering if anybody knows the references for this change. Here is the difference between the two distributions: diff ~/TEST/gromacs-3.3/share/top/ffoplsaa.rtp ~/TEST/gromacs-3.3.1/share/top/ffoplsaa.rtp 1008,1010c1008,1010 CDCENZ HZ1dih_LYSH_chi5_C_C_N_H CDCENZ HZ2dih_LYSH_chi5_C_C_N_H CDCENZ HZ3dih_LYSH_chi5_C_C_N_H --- CDCENZ HZ1dih_LYS_chi5_C_C_N_H CDCENZ HZ2dih_LYS_chi5_C_C_N_H CDCENZ HZ3dih_LYS_chi5_C_C_N_H 1025c1025 CGopls_2100.09753 --- CGopls_2100.048 3 1028,1029c1028,1029 SDopls_202 -0.435 4 CEopls_2090.03755 --- SDopls_202 -0.335 4 CEopls_209 -0.013 5 1325,1326c1325,1326 NCACBCGdih_GLU_chi1_N_C_C_C CGCBCA Cdih_GLU_chi1_C_C_C_CO --- NCACBCGdih_TRP_chi1_N_C_C_C CGCBCA Cdih_TRP_chi1_C_C_C_CO ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Doubt in Distance Restraints
Hi Raja,You may be better off just adding bonds. I believe there was a bond type (type 6) which was especially useful (intended?) for keeping metals bound to a protein.Cheers,Tsjerk On 4/20/06, raja [EMAIL PROTECTED] wrote: Dear all,My intention is to restrict Fe(II) in active site by distancerestraint protocol. Fe(II) is ligated by three amino acides' polaratoms respectively by (1) NE2 of HIS ,(2) NE2 of HIS (3) OD1 of ASP. The following is the disres itp file I used (copied frommanual3.3). where I edited the atom number ofaminoacids(3724,2839,2872) and Fe(II) as 4734.# disres.itp #[ distance restraints ]; ai ajtypeindextype' low up1 up2 fac 37244734 1010.0 2.090.4 1.0 28394734 1010.02.250.4 1.0 28724734 1010.02.180.4 1.0 I do not understand the meaning of up2 and fac so I left with 0.4and1.0 as such as found in manual.In mdp file I added the following the commands## full.mdp## define = -DDISRESdisre= Simple###I expected these modifictions will restrict but those distances are not restraintedwhy ?Kindly explain me that wheather I need to change any other parameter .With thanks !B.Nataraj--raja[EMAIL PROTECTED] --http://www.fastmail.fm - IMAP accessible web-mail___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of GroningenNijenborgh 49747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Doubt in Distance Restraints
Raja, distance retraints are described in the manual (Section 4.3.4). The potential form is given in Figure 4.13 (Gromacs 3.3 manual). There you can find out what low (r0), up1 (r1) and up2 (r2) mean. I also want to remind you that the distances are given in nanometers. Hence the allowed unpenalized distance between atoms 3724 and 4734 as you defined it would be 20.9 angstroms, which probably not what you want. Best regards, Uwe raja wrote: Dear all, My intention is to restrict Fe(II) in active site by distance restraint protocol. Fe(II) is ligated by three amino acides' polar atoms respectively by (1) NE2 of HIS ,(2) NE2 of HIS (3) OD1 of ASP. The following is the disres itp file I used (copied from manual3.3). where I edited the atom number of aminoacids(3724,2839,2872) and Fe(II) as 4734. # disres.itp # [ distance restraints ] ; ai ajtypeindextype’ low up1 up2 fac 3724 4734 1010.0 2.09 0.4 1.0 2839 4734 1010.0 2.25 0.4 1.0 2872 4734 1010.0 2.18 0.4 1.0 I do not understand the meaning of up2 and fac so I left with 0.4 and 1.0 as such as found in manual. In mdp file I added the following the commands ## full.mdp ## define = -DDISRES disre= Simple ### I expected these modifictions will restrict but those distances are not restraintedwhy ? Kindly explain me that wheather I need to change any other parameter . With thanks ! B.Nataraj ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] NS in PME
Hello Berk and David! Could you explain why we shouldnt use rlistrcoulomb with PME. To my knowledge good energy conservation will be achieved only with this combination because diffusion between successive NS will be taken into account. Michael Shirts agreed with this on gmx-developers mailing list: http://www.gromacs.org/pipermail/gmx-developers/2006-April/001581.html but atleast I didnt understand from Berks response the fundamental basis for the restriction to rlist=rcoulomb. Manual of Amber8 also recommends use of larger NS cut-off than real space cut-off with PME so that energy conservation will be achieved: NBFLAG: If nbflag = 0, construct the direct sum nonbonded list in the old way, i.e. update the list every nsnb steps. If nbflag = 1 (the default when imin = 0 or ntb 0), nsnb is ignored, and the list is updated whenever any atom has moved more than 1/2 skinnb since the last list update. SKINNB: Width of the nonbonded skin. The direct sum nonbonded list is extended to cut + skinnb, and the van der Waals and direct electrostatic interactions are truncated at cut. Default is 2.0 Å. Use of this parameter is required for energy conservation, and recommended for all PME runs. Thanks for any comments in advance! Janne -- Janne Hirvi, MSc(Physical Chemistry), Researcher University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI Tel: +358 13 2514544 +358 50 3474223 E-mail: [EMAIL PROTECTED] [EMAIL PROTECTED] -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] REMD
hi, How can I REMD simulation in GROMACS 3.2?Best, Jahanshah Blab-away for as little as 1¢/min. Make PC-to-Phone Calls using Yahoo! Messenger with Voice.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] REMD
jahanshah ashkani wrote: hi, How can I REMD simulation in GROMACS 3.2? not. use 3.3.1 Best, Jahanshah Blab-away for as little as 1¢/min. Make PC-to-Phone Calls http://us.rd.yahoo.com/mail_us/taglines/postman2/*http://us.rd.yahoo.com/evt=39663/*http://voice.yahoo.com using Yahoo! Messenger with Voice. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] REMD
jahanshah ashkani wrote: hi, How can I REMD simulation in GROMACS 3.2? You can't. REMD didn't come until 3.3 - and the gromacs manual is the place to start looking. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Please Help: Still facing problems with installing Gromacs 3.3.1 on SGI Irix
Hi,
I met the same kind of problem with gromacs 3.2.1, and could quickly fix
it, by replacing e.g.
{ evStepOptions[evLINFIX], FALSE, etSTR, {evParams[evLINFIX]}, == {
-linfix, FALSE, etSTR, {evSelections[evLINFIX]}, etc...
See http://www.gromacs.org/pipermail/gmx-users/2004-May/010404.html
Patrick
Akshay Patny a écrit :
SUBJECT: Still facing problems with installing Gromacs 3.3.1 on SGI Irix
Hi
As suggested by Dr. Spoel, I removed one of the semicolons before the
double semicolon in one of the lines in the file gmx_chi.c
I re-installed again and this time it gave me the following error. Can
you suggest what is going wrong and how can I fix it now?
cc-1028 cc: ERROR File = make_edi.c, Line = 579
The expression used must have a constant value.
{ evStepOptions[evLINFIX], FALSE, etSTR, {evParams[evLINFIX]},
^
cc-1028 cc: ERROR File = make_edi.c, Line = 581
The expression used must have a constant value.
{ evStepOptions[evLINACC], FALSE, etSTR, {evParams[evLINACC]},
^
cc-1028 cc: ERROR File = make_edi.c, Line = 583
The expression used must have a constant value.
{ evStepOptions[evRADFIX], FALSE, etREAL, {radfix},
^
cc-1552 cc: WARNING File = make_edi.c, Line = 622
The variable bTop is set but never used.
bool bTop, bM, bFit1;
^
3 errors detected in the compilation of make_edi.c.
*** Error code 2 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
I really appreciate your help.
Kind Regards
Akshay
Akshay Patny
**Akshay Patny***
*
**Graduate Research Assistant**
Faser Hall 417, Department of Medicinal Chemistry
Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
Tel: 662-915-1286 (office); Web: www.olemiss.edu http://www.olemiss.edu
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--
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Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INSERM U726, Universite Paris 7
Case Courrier 7113
2, place Jussieu, 75251 Paris Cedex 05, FRANCE
Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30
E-mail : [EMAIL PROTECTED]
Web Site: http://www.ebgm.jussieu.fr/~fuchs
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Re: [gmx-users] FFTW installation error: cannot compile asimpleFortran program
Dear Florian, Thanks for your help. The installation of FFTW3 source code does work by setting the prefix. Then, I have set LDFLAGS and CPPFLAGS to install Gromacs from gromacs-3.3.1-1.src.rpm. However, there is an error when installing Gromacs: $ rpmbuild -rebuild gromacs-3.3.1-1.src.rpm ... ... checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library error: Bad exit status from /var/tmp/rpm-tmp.67043 (%build) RPM build errors: user erikli does not exist - using root group el does not exist - using root user erikli does not exist - using root group el does not exist - using root Bad exit status from /var/tmp/rpm-tmp.67043 (%build) I can only find fftw3.f under ./fftw/include. Don't know what fftw3f is. Sunny From: Florian Haberl [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] FFTW installation error: cannot compile asimpleFortran program Date: Wed, 19 Apr 2006 18:27:16 +0200 hi, simple install first fftw with: grep fftw from fftw site wget http://www.fftw.org/fftw-3.1.1.tar.gz unpack ./configure --prefix=/hereyourdirectorywhereyoucanwrite make make install than do: setenv LDFLAGS -L/raid1/haberl/bin/fftw/3.0.1-32/lib setenv CPPFLAGS -I/raid1/haberl/bin/fftw/3.0.1-32/include (change your lib and include directory to the one above) than configure gromacs if fortran doesn`t work try a --disable-fortran On Wednesday 19 April 2006 15:57, Ge Sunny wrote: From: Ge Sunny [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: Re: [gmx-users] FFTW installation error: cannot compile a simpleFortran program Date: Wed, 19 Apr 2006 13:32:14 + To Mark: I use the binary fftw3-3.0.1-4 on FC4 with no complaints. Why not use it? There is another problem. I'm not root. Running from binary pack has an error: error: can't create transaction lock on /var/lib/rpm/__db.000 I have tried creating .rpcmacros and all ./rpm subdirectories under my home directory, then run rpm. The error above still occurs. Sorry. I mean .rpmmacros is created which includes: %_topdir my_home/rpm Then run rpm -ivh fftw3-3.0.1-4.x86_64.rpm. It causes error: can't create transaction lock on /var/lib/rpm/__db.000 because I don't have root permission. Sunny _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 _ Express yourself instantly with MSN Messenger! Download today - it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] FFTW installation error: cannot compile asimpleFortran program
Hi, On Apr 20, 2006, at 12:25 PM, Ge Sunny wrote: Dear Florian, Thanks for your help. The installation of FFTW3 source code does work by setting the prefix. Then, I have set LDFLAGS and CPPFLAGS to install Gromacs from gromacs-3.3.1-1.src.rpm. However, there is an error when installing Gromacs: $ rpmbuild -rebuild gromacs-3.3.1-1.src.rpm ... ... checking for fftw3.h... yes checking for main in -lfftw3f... no configure: error: Cannot find fftw3f library error: Bad exit status from /var/tmp/rpm-tmp.67043 (%build) RPM build errors: user erikli does not exist - using root group el does not exist - using root user erikli does not exist - using root group el does not exist - using root Bad exit status from /var/tmp/rpm-tmp.67043 (%build) I can only find fftw3.f under ./fftw/include. Don't know what fftw3f is. The single precision FFTW3 library. You probably didn't include -- enable-float. Go through the detailed instructions at http://www.gromacs.org/installation/prerequisites.php Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Drug Enzyme Tutorial - mdrun segmentation fault
Hi Tom, and thankyou very much! The workaround didn't work but I udgraded to Gromacs 3.3.1 and now I get mdrun running correctly. -Simone This is probably the result of a bug in 3.3, fixed in 3.3.1. Setting pme_order = 4 is a workaround in case you don't want to upgrade to 3.3.1. --Tom On Apr 19, 2006, at 11:05 AM, Zorzan Simone wrote: Hi all, I am trying to do the Drug Enzyme tutorial (trp_drug_tutor.pdf), on a linux box (suse 10.0) and Gromacs 3.3. Everything is fine until this command: nohup mdrun -s trp_pr.tpr -o trp_pr.trr -c trp_b4md.gro -g pr.log - e pr.edr That ends abnormally with a segmentation fault. I searched the mailing list archive but I didn't find anything helpful. Has anybody tried this tutorial with Gromacs 3.3 (it's tested on 3.2.1)? Any help is greatly appreciated. Zorzan Simone. pr.mdp, mdout.mdp and pr.log follows. pr.mdp title = trp_drg warnings= 10 cpp = /lib/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20.0 ps. nstcomm =1 nstxout = 250 ; output coordinates every 0.5 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout =0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx=0 fourier_ny=0 fourier_nz=0 pme_order =6 ewald_rtol= 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.10.1 0.1 0.1 tc_grps = proteinsol IN4 Cl ref_t = 300300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 == mdout.mdp == ; ;File 'mdout.mdp' was generated ;By user: simone (1000) ;On host: linux ;At date: Wed Apr 19 16:52:27 2006 ; ; VARIOUS PREPROCESSING OPTIONS title= trp_drg ; Preprocessor - specify a full path if necessary. cpp = /lib/cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 1 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 250 nstvout = 1000 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 10 nstenergy= 10 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME
[gmx-users] OPLS modification between 3.3 and 3.3.1??
Thank you Erik and Mark for your assistance. Appologies that I reposted an old question. I will be more diligent about my searches in the future. Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] Unnatural amino acid problems
Hello Mark Thanks for your comments. I realise that putting in zeros would not give me a good model. That's why I am putting in parameters in the .top file based on the atom types, which I get from the ffoplsaabon.itp file. But the distortion still persists, and in fact sometimes gets worse (at least visually), which is bizarre. I can only think of one one more thing that could be the reason; is the .top file formatted? So for example, if I put in the parameters for a dihedral, does each one of the numbers have to be exactly below c0,c1,c2,c3 etc.? Thanks Ashutosh On Apr 20, 2006, at 12:41 AM, Mark Abraham wrote: Hello I am parametrizing an unnatural amino acid, phenylglycine (PHG), in the OPLS FF in GROMACS. I have put in the necessary parameters in the .hdb, .rtp, and the aminoacids.dat file. 1. When I do grompp for the EM, I get an error saying that I have not put in the appropriate parameters for the bonds, angles and dihedrals. Well that means you haven't done it :-) Go back and compare what you've done for PHG with other amino acids, see what is different and fix it. Surprisingly, when I do put in the parameters (from the ffoplsaabon.itp file), the angles, bonds, and dihedrals get even more distorted, a counterintuitive observation. In fact the simulation is much better off when I ignore the warnings and the program puts in zeros after the required parameters in the .top file. Why is this happening? You can't tell that your force field is a reasonable physical model by looking at the results on their own - you need a comparison with experiment. Often you can tell by looking at the results that it is completely wrong, however. Just putting in zeroes guarantees you a spurious model, whether you can recognise that from the results or not. Another question related to this: 2. When I do parametrize a single peptide with a single PHG residue and then simulate it (with zeros for the parameters in the .top file), the PHG turns out fine and does not get distorted. But when I simulate many PHG containing peptides, say 10 of them stacked on top of and besides each other, I observe that some of the PHGs get distorted while others don't. By distorted, I especially mean the Halpha-Calpha-aromaticC angle, which gets distorted to almost 90 from its normal value of about 109. Whatever the cause for this distortion is, why is it affecting only some PHG residues and not others? It's a stochastic system... run it for long enough and you'll see weird stuff everywhere. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] Parralel Gromacs
Hi everybody, First let me introduce myself. My name is Nicu Goga and I am currentely working at the Univeristy of Groningen, Biomolecular group as a Gromacs developer. I am quite new into this field. I have some questions related to Gromacs. Can anyone help me with these questions? I thank you in advance. 1) Is anyone working still on a paralel version of Gromacs? If yes, please tell me, maybe we can join the efforts. 2) Which things do you think that can be still improved regarding parallel Gromacs. 3) I installed the last version of Gromacs found on the webpage (version 3.3.1). Whice are the source files in C (where I can have a look) where the paralel version of Gromacs is implemented. I thank you in advance for your answers. Best regards Nicu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] Subject: Interfacial System - Topology file
Hi everybody, I'm trying GROMACS by the 1st time with an interfacial system: HFA and Water. I had created the topology file manually and the HFA section had worked fine for an energy minimization of pure HFA and air. However, the geometry of HFA molecules become distorted during interfacial energy minimization, but the box doesn't collapse. I can see from VMD visualization package that the geometry is distorted. I would like to know if there is anything wrong with my topol.top file (described bellow). I had added the opls atoms and LJ parameters in the ffoplsanb.itp and; bonds, angles and dihedral in ffoplsaabon.tip. Since initially I'm trying to simplify the system, my HFA molecules will have a rigid geometry. So, angles and dihedral specifications became comments in the ffoplsaabon.tip file. Pls, let me know if I'm in the right track. Thanks #include ffoplsaa.itp [ moleculetype ] ; molnamenrexcl SOL2 [ atoms ] ; nr type resnr residue atom cgnr charge 1opls_970 1SOLHW1 1 0.4238 2opls_971 1SOLHW2 1 0.4238 3opls_972 1SOLOW 1-0.8476 [ bonds ] ; ijfunct 311 321 [ angles ] ; ijk 132 [ moleculetype ] ; name nrexcl HFA3 [ atoms ] ; nr type resnr residue atom cgnr charge 1 opls_966 1HFAFF 1-0.30 2 opls_967 1HFACH 1 0.24 3 opls_969 1HFAHF 1 0.03 4 opls_969 1HFAHF 1 0.03 5 opls_968 1HFACF 1 0.90 6 opls_966 1HFAFF 1-0.30 7 opls_966 1HFAFF 1-0.30 8 opls_966 1HFAFF 1-0.30 [ constraints ] ; aiaj funct b0 1 2 1 0.13600 3 2 1 0.10900 4 2 1 0.10900 2 5 1 0.15290 5 6 1 0.13600 5 7 1 0.13600 5 8 1 0.13600 1 4 1 0.20228 3 4 1 0.17695 8 1 1 0.28042 8 6 1 0.22022 6 7 1 0.22028 6 4 1 0.32963 [ system ] HFA and water [ molecules ] SOL735 HFA 156 -- Robson Peguin, PhD Student Wayne State University, ChE Detroit - MI, 48201 - USA 2015 MEB, (313) 577-1416 2348 ENG, (313) 577-5765 Fax: (313) 577-3810 e-mail: [EMAIL PROTECTED] http://chem1.eng.wayne.edu/~sdr/ _ Robson P. S. Peguin, PhD Student Wayne State University Department of Chemical Engineering and Materials Science Detroit - MI, 48201 - USA 2015 MBE, phone: (313) 577-1416 2348 ENG, phone: (313) 577-5765 Fax: (313)577-3810 e-mail: [EMAIL PROTECTED] http://chem1.eng.wayne.edu/~sdr/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
