Hi Pavan, Please, I'm not a user list. This is in no way attached to the tutorials of mine.
But your problem arises because you're mixing things up. You're using a new run input (.tpr) file, and a checkpoint (.cpt) file. Either you continue runs using checkpoint files (preferred) or you generate a new .tpr file and use that, leaving the checkpoint file. This could for instance be done because you want to change the output frequency for some block. The .part***. addition is added because you don't give the option -append, that would otherwise cause the subsequent trajectory/energy stuff be appended to already existing files. Without that option, gromacs adds a part identifier to avoid overwriting existing files. Cheers, Tsjerk On Wed, Dec 23, 2009 at 10:14 PM, Pavan Ghatty <pavangha...@gmail.com> wrote: > Restarts are still a cause of heart-burn Tsjerk. > I have these files at the moment: > 1ea5.grompp4.cpt > 1ea5.grompp4.edr > 1ea5.grompp4.gro > 1ea5.grompp4.log > 1ea5.grompp4.tpr > 1ea5.grompp4.trr > md.mdp --> http://compbio.ornl.gov/~pkc/md.txt > The aim for now is to generate a bunch of 5ps trajectory files that look > like 1ea5.grompp[4-100].trr .I will then use trjcat to concatenate all the > .trr files. From my understanding mdrun needs .tpr (only topology is read) > and .cpt files to extend a simulation. > > tpbconv -s ./1ea5.grompp4.tpr -f ./1ea5.grompp4.trr -e ./1ea5.grompp4.edr -o > ./1ea5.grompp5.tpr > > This gave ./1ea5.grompp5.tpr with > nsteps = 5000 > and such. > > Then, > mdrun -v -s ./1ea5.grompp5.tpr -cpi ./1ea5.grompp4.cpt -deffnm > ./1ea5.grompp5 > gave me, > 1ea5.grompp5.tpr > 1ea5.grompp5.part0002.xtc > 1ea5.grompp5.part0002.trr > 1ea5.grompp5.part0002.log > 1ea5.grompp5.part0002.gro > 1ea5.grompp5.part0002.edr > 1ea5.grompp5.cpt > > I don't understand why the output of xtc/trr/log is not > 1ea5.grompp5.(xtc/trr/log). This creates a problem with the next script > which looks like: > tpbconv -s ./1ea5.grompp5.tpr -f ./1ea5.grompp5.trr -e ./1ea5.grompp5.edr -o > ./1ea5.grompp6.tpr -extend 5 > and so on. Just to see what happens I did > tpbconv -s 1ea5.grompp5.tpr -f ./1ea5.grompp5.part002.trr -e > ./1ea5.grompp5.part0002.edr -o ./1ea5.grompp6.tpr -extend 5 > and ran > mdrun -v -s ./1ea5.grompp6.tpr -cpi ./1ea5.grompp5.cpt -deffnm > ./1ea5.grompp6 > > This gave > 1ea5.grompp6.part0003.xtc > 1ea5.grompp6.part0003.trr > 1ea5.grompp6.part0003.log > 1ea5.grompp6.part0003.gro > 1ea5.grompp6.part0003.edr > > What am I doing wrong? > g_energy -f 1ea5.grompp5.part0002.edr -o temp.xvg [total energy] gave > 2.000000 > -834920.625000 > 3.000000 -831025.187500 > 4.000000 -829585.187500 > 5.000000 -828792.437500 > g_energy -f 1ea5.grompp6.part0003.edr -o temp.xvg [total energy] gave > 5.000000 -828792.500000 > 6.000000 -828115.000000 > 7.000000 -828224.312500 > 8.000000 -827586.187500 > 9.000000 -828065.500000 > 10.000000 -828509.125000 > Since the energies at step 5.000 are (almost) the same from grompp5.trr and > grompp6.trr, can I assume that the simulation is reliably moving forward? > The trajectories at this time are too small to notice any jumps. > > Pavan > > On Tue, Dec 22, 2009 at 9:05 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> >> Hi Pavan, >> >> The first thing is to formulate your research question. Second you >> have to determine which tools are best suited to investigate and >> answer that question. Third, you have to determine how to use these >> tools optimally to answer the question. >> In your study you also have to consider how others have addressed the >> same or similar issues previously and reflect on the correctness of >> their approach. >> That is about as specific as I can answer your question, as you >> haven't given a formulation of your question. Aside from that, note >> that your best option is likely to consist of several approaches >> combined, and reflect on commonalities and differences between these. >> In your case that would come down to performing simulations with both >> 43a1/43a2 and 45a3. That will allow you to put the results from the >> earlier study in scope. >> >> Cheers, >> >> Tsjerk >> >> On Mon, Dec 21, 2009 at 3:56 PM, Pavan Ghatty <pavangha...@gmail.com> >> wrote: >> > Sorry I hit the send button by mistake. >> >> >> >> Hi Tsjerk, >> >> I managed to run the simulation over the weekend. But the question of >> >> forcefield kept bothering me. Especially the attached paper. The aim of >> >> my >> >> simulation is to see the flexibility of the aromatic residues (chi_1 >> >> chi_2) >> >> of 1ea5 in water at 300K. Page 12 of the paper attached is particularly >> >> worrisome. An earlier paper on the topic titled "Flexibility of >> >> aromatic >> >> residues in the active-site gorge of Acetylcholinesterase: X-ray vs >> >> molecular dynamics" published in 2008 used 43a1 ff. For the purposes of >> >> this >> >> simulation does it really matter which ff I use? I wrote to authors of >> >> that >> >> paper and I was simply referred to the Gromacs manual for information. >> >> Now I >> >> am completely confused. >> > >> > Thanks, >> > Pavan >> > >> > >> >> >> >> On Wed, Dec 16, 2009 at 1:06 PM, Tsjerk Wassenaar <tsje...@gmail.com> >> >> wrote: >> >>> >> >>> Hi Pavan, >> >>> >> >>> For me, the easy way out is this: The GROMOS FFs are parameterized >> >>> with, and thus to be used with, SPC type solvent. The conditions used >> >>> to derive a force field are in a sense part of that force field. Using >> >>> TIP* solvent models with GROMOS is basically mixing force fields, >> >>> which is considered bad practice. >> >>> >> >>> Cheers, >> >>> >> >>> Tsjerk >> >>> >> >>> On Wed, Dec 16, 2009 at 5:54 PM, Pavan Ghatty <pavangha...@gmail.com> >> >>> wrote: >> >>> > Hi Tsjerk, >> >>> > I managed to solvate the protein in tip3p water. to addions I need a >> >>> > .trp >> >>> > file which comes from grompp. Now grompp with minim.mdp file from >> >>> > http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ dies with this >> >>> > error >> >>> > "atomtype OWT3 not found". >> >>> > http://www.mail-archive.com/gmx-users@gromacs.org/msg15722.html has >> >>> > some >> >>> > info on it but I cannot figure out how to resolve it. The ff I am >> >>> > using >> >>> > ff45a3nb.itp does not have OWT3 atomtype in it. But the file >> >>> > tip3p.itp >> >>> > does >> >>> > have OWT3 atomtype. The message grompp printed out are at >> >>> > http://compbio.ornl.gov/~pkc/error. You can see in the file that the >> >>> > program >> >>> > does read the file tip3p.itp. >> >>> > How do I make grompp recognize TIP3P water and OWT3 atomtype? >> >>> > Thanks and sorry for bugging you. I'll keep it short. >> >>> > Pavan >> >>> > >> >>> > >> >>> > On Tue, Dec 15, 2009 at 11:19 AM, Tsjerk Wassenaar >> >>> > <tsje...@gmail.com> >> >>> > wrote: >> >>> >> >> >>> >> Hi Pavan, >> >>> >> >> >>> >> You can make local copies of such files in the working directory, >> >>> >> which will get precedence over the global ones. >> >>> >> >> >>> >> Cheers, >> >>> >> >> >>> >> Tsjerk >> >>> >> >> >>> >> On Tue, Dec 15, 2009 at 4:49 PM, Pavan Ghatty >> >>> >> <pavangha...@gmail.com> >> >>> >> wrote: >> >>> >> > Hi Tsjerk, >> >>> >> > I used AMBER to get the structure, then used VMD to strip the >> >>> >> > hydrogens. >> >>> >> > Now >> >>> >> > pdb2gmx gave me a .gro and .top file but seems to have detected a >> >>> >> > total >> >>> >> > negative charge of 7 while AMBER and CHARMM (using >> >>> >> > NAMD/VMD/CHARMM27 >> >>> >> > ff) >> >>> >> > both detected -9. I am wondering how to overcome this problem. >> >>> >> > There >> >>> >> > is >> >>> >> > also >> >>> >> > a problem with disulphide bonds. I did use the -merge option with >> >>> >> > pdb2gmx >> >>> >> > but the Cysteine sulphurs have hydrogens anyway in the .gro >> >>> >> > >> >>> >> > >> >>> >> > file. http://www.gromacs.org/Documentation/File_Formats/specbond.dat has >> >>> >> > some information on how to deal with the issue but the >> >>> >> > specbond.dat >> >>> >> > file >> >>> >> > seems to be in /usr/local/gromacs...location which is accessible >> >>> >> > only by >> >>> >> > root and here in the lab (oh btw I am a post-doc in Oak Ridge >> >>> >> > National >> >>> >> > Laboratory) very few people are given root access. Is there a way >> >>> >> > to >> >>> >> > make >> >>> >> > pdb2gmx read specbond.dat file? >> >>> >> > Thanks! >> >>> >> > On Tue, Dec 15, 2009 at 10:19 AM, Tsjerk Wassenaar >> >>> >> > <tsje...@gmail.com> >> >>> >> > wrote: >> >>> >> >> >> >>> >> >> Hi Pavan, >> >>> >> >> >> >>> >> >> With AMBER you probably added all hydrogens, which would make >> >>> >> >> pdb2gmx >> >>> >> >> complain about hydrogen atoms that are not listed in the >> >>> >> >> building >> >>> >> >> blocks for the GROMOS FFs, which are united atom FFs. If that is >> >>> >> >> the >> >>> >> >> case, you can add -ignh on the command line to have Gromacs >> >>> >> >> strip >> >>> >> >> off >> >>> >> >> all hydrogens present and rebuild only those needed according to >> >>> >> >> the >> >>> >> >> force field. >> >>> >> >> >> >>> >> >> Cheers, >> >>> >> >> >> >>> >> >> Tsjerk >> >>> >> >> >> >>> >> >> On Tue, Dec 15, 2009 at 4:11 PM, Pavan Ghatty >> >>> >> >> <pavangha...@gmail.com> >> >>> >> >> wrote: >> >>> >> >> > Hi Tsjerk, >> >>> >> >> > Thanks for the reply. I used AMBER to get the proper structure >> >>> >> >> > and >> >>> >> >> > pdb2gmx still fails. I will try a few more times and if it >> >>> >> >> > still >> >>> >> >> > fails >> >>> >> >> > I'll drop a line to gmx-users list. >> >>> >> >> > Cheers! >> >>> >> >> > >> >>> >> >> > On 12/14/09, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> >>> >> >> >> Hi Pavan, >> >>> >> >> >> >> >>> >> >> >> At the beginning of the tutorial you have to check whether >> >>> >> >> >> your >> >>> >> >> >> structure is missing residues and/or side chain atoms. The >> >>> >> >> >> error >> >>> >> >> >> message from pdb2gmx indicates that side chain atoms are >> >>> >> >> >> missing. >> >>> >> >> >> You >> >>> >> >> >> will have to build these in some way first. >> >>> >> >> >> >> >>> >> >> >> By the way, it's not the Gromacs FF. It's GROMOS96, from the >> >>> >> >> >> Van >> >>> >> >> >> Gunsteren group in Zurich. Gromacs doesn't really have a >> >>> >> >> >> force >> >>> >> >> >> field >> >>> >> >> >> of its own. For what it's worth, I'd also stick with the >> >>> >> >> >> Gromos >> >>> >> >> >> 45a3 >> >>> >> >> >> force field, rather than taking 53a6. My experiences with the >> >>> >> >> >> latter >> >>> >> >> >> are not very good. >> >>> >> >> >> >> >>> >> >> >> As a final note, it is better to post questions like these to >> >>> >> >> >> the >> >>> >> >> >> gmx-users list. I'm on there, but so are many more. That will >> >>> >> >> >> ensure >> >>> >> >> >> that you receive answers quicker and probably better. >> >>> >> >> >> >> >>> >> >> >> Best, >> >>> >> >> >> >> >>> >> >> >> Tsjerk >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> On Mon, Dec 14, 2009 at 5:13 PM, Pavan Ghatty >> >>> >> >> >> <pavangha...@gmail.com> >> >>> >> >> >> wrote: >> >>> >> >> >>> Hello Tsjerk, >> >>> >> >> >>> >> >>> >> >> >>> I need a small favor with preparing a simulation box with >> >>> >> >> >>> protein >> >>> >> >> >>> (1ea5 >> >>> >> >> >>> has >> >>> >> >> >>> a net negative charge of 9) in a box of water with 9 sodium >> >>> >> >> >>> ions. I >> >>> >> >> >>> am >> >>> >> >> >>> using >> >>> >> >> >>> your tutorial at >> >>> >> >> >>> http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ >> >>> >> >> >>> as >> >>> >> >> >>> a >> >>> >> >> >>> reference. >> >>> >> >> >>> >> >>> >> >> >>> I got 1ea5.pdb from PDB and used the following set of >> >>> >> >> >>> commands. >> >>> >> >> >>> mv 1ea5.pdb 1ea5.pdb.org >> >>> >> >> >>> grep -v NAG 1ea5.pdb.org > 1ea5.pdb >> >>> >> >> >>> pdb2gmx -f 1ea5.pdb -o 1ea5.gro -p 1ea5.top -water tip3p >> >>> >> >> >>> Selected ff53a6. >> >>> >> >> >>> Error/output: >> >>> >> >> >>> >> >>> >> >> >>> 1. It correctly identified the three disulphide bonds I am >> >>> >> >> >>> interested >> >>> >> >> >>> it >> >>> >> >> >>> CYS64 CYS91 CYS228 CYS251 CYS262 >> >>> >> >> >>> CYS399 >> >>> >> >> >>> SG489 SG709 SG1757 SG1934 SG2022 >> >>> >> >> >>> SG3103 >> >>> >> >> >>> CYS91 SG709 !0.204! >> >>> >> >> >>> CYS262 SG2022 2.226 2.157 3.288 !0.203! >> >>> >> >> >>> CYS518 SG4098 3.269 3.463 1.117 4.102 4.286 >> >>> >> >> >>> !0.205! >> >>> >> >> >>> >> >>> >> >> >>> 2. Making bonds... >> >>> >> >> >>> Opening library file >> >>> >> >> >>> /share/build/gromacs-4.0.5/share/top/aminoacids.dat >> >>> >> >> >>> >> >>> >> >> >>> WARNING: atom CE is missing in residue LYSH 11 in the pdb >> >>> >> >> >>> file >> >>> >> >> >>> WARNING: atom NZ is missing in residue LYSH 11 in the pdb >> >>> >> >> >>> file >> >>> >> >> >>> WARNING: atom HZ1 is missing in residue LYSH 11 in the pdb >> >>> >> >> >>> file >> >>> >> >> >>> You might need to add atom HZ1 to the hydrogen >> >>> >> >> >>> database of >> >>> >> >> >>> residue >> >>> >> >> >>> LYSH >> >>> >> >> >>> in the file ff???.hdb (see the manual) >> >>> >> >> >>> WARNING: atom CG is missing in residue ASN 39 in the pdb >> >>> >> >> >>> file >> >>> >> >> >>> WARNING: atom HD22 is missing in residue ASN 39 in the pdb >> >>> >> >> >>> file >> >>> >> >> >>> You might need to add atom HD22 to the hydrogen >> >>> >> >> >>> database >> >>> >> >> >>> of >> >>> >> >> >>> residue >> >>> >> >> >>> ASN >> >>> >> >> >>> in the file ff???.hdb (see the manual) >> >>> >> >> >>> >> >>> >> >> >>> 3. After 44 such warnings it dies with this error: >> >>> >> >> >>> ------------------------------------------------------- >> >>> >> >> >>> Program pdb2gmx, VERSION 4.0.5 >> >>> >> >> >>> Source code file: pdb2top.c, line: 704 >> >>> >> >> >>> >> >>> >> >> >>> Fatal error: >> >>> >> >> >>> There were 44 missing atoms in molecule Protein_A, if you >> >>> >> >> >>> want >> >>> >> >> >>> to >> >>> >> >> >>> use >> >>> >> >> >>> this >> >>> >> >> >>> incomplete topology anyhow, >> >>> >> >> >>> use the option -missing >> >>> >> >> >>> ------------------------------------------------------- >> >>> >> >> >>> >> >>> >> >> >>> Could you please help in understand where I am going wrong? >> >>> >> >> >>> I >> >>> >> >> >>> am >> >>> >> >> >>> more >> >>> >> >> >>> used >> >>> >> >> >>> to running simulations in Amber and NAMD but I am currently >> >>> >> >> >>> in >> >>> >> >> >>> a >> >>> >> >> >>> rather >> >>> >> >> >>> tight situation where my boss wanted to test a simulation >> >>> >> >> >>> with >> >>> >> >> >>> Gromacs >> >>> >> >> >>> ff. >> >>> >> >> >>> I >> >>> >> >> >>> know NAMD can run on Gromacs ff but I will still need >> >>> >> >> >>> Gromacs >> >>> >> >> >>> inputs >> >>> >> >> >>> for >> >>> >> >> >>> that >> >>> >> >> >>> [http://www.ks.uiuc.edu/Research/namd/2.7b2/ug/node15.html]. >> >>> >> >> >>> Any >> >>> >> >> >>> help >> >>> >> >> >>> will be greatly appreciiated. >> >>> >> >> >>> Thanks! >> >>> >> >> >>> >> >>> >> >> >>> -- >> >>> >> >> >>> Pavan K. Ghatty >> >>> >> >> >>> >> >>> >> >> >>> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> -- >> >>> >> >> >> Tsjerk A. Wassenaar, Ph.D. >> >>> >> >> >> >> >>> >> >> >> Computational Chemist >> >>> >> >> >> Medicinal Chemist >> >>> >> >> >> Neuropharmacologist >> >>> >> >> >> >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > -- >> >>> >> >> > Pavan K. Ghatty >> >>> >> >> > >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> -- >> >>> >> >> Tsjerk A. Wassenaar, Ph.D. >> >>> >> >> >> >>> >> >> Computational Chemist >> >>> >> >> Medicinal Chemist >> >>> >> >> Neuropharmacologist >> >>> >> > >> >>> >> > >> >>> >> > >> >>> >> > -- >> >>> >> > Pavan K. Ghatty >> >>> >> > >> >>> >> > >> >>> >> >> >>> >> >> >>> >> >> >>> >> -- >> >>> >> Tsjerk A. Wassenaar, Ph.D. >> >>> >> >> >>> >> Computational Chemist >> >>> >> Medicinal Chemist >> >>> >> Neuropharmacologist >> >>> > >> >>> > >> >>> > >> >>> > -- >> >>> > Pavan K. Ghatty >> >>> > >> >>> > >> >>> >> >>> >> >>> >> >>> -- >> >>> Tsjerk A. Wassenaar, Ph.D. >> >>> >> >>> Computational Chemist >> >>> Medicinal Chemist >> >>> Neuropharmacologist >> >> >> >> >> >> >> >> -- >> >> Pavan K. Ghatty >> >> >> > >> > >> > >> > -- >> > Pavan K. Ghatty >> > >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> Computational Chemist >> Medicinal Chemist >> Neuropharmacologist > > > > -- > Pavan K. Ghatty > > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
