[gmx-users] water Mediated Hydrogen Bond
Dear all I have been looking for water mediated hydrogen bond in my simulation when i use g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond in gromacs ? is there any way to calculate hydrogen mediated hydrogen bond. Thanking you E R Azhagiya singam -- gmx-users mailing listgmx-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
Re: [gmx-users] Grompp error: No default g96angle type
HI I am using Cytochrome-C pdb 1hrc.pdb. In pdb2gmx it does not gives any eror using ffG43a1. .top file produced shows all bonds (Fe SD of MET 80 and Fe NE2 of HIS 18) using spec.dat file but all the error lines does not have bond/angle nomenclature such as 809 810 2gb_30 810 811 2gb_29 810 1068 2 812 813 2gb_4 812 814 2gb_9 814 815 2gb_2 810 atom SD of MET80 and 1068 is Fe of Heme. I tried modifying .rtp file of force-field and adding these bonds and giving some name to it but got the same error in grompp. Though .top file shows these bonds the .gro file generated does not show these bonds in VMD while original pdb file shows these bonds. thanking you. waiting for your suggestion. shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin These errors are from bond between MET/HIS residue and Heme group of my protein. I checked for all these nine errors of bond and angle in th file ffG43a1bon.itp and I couldnt find these defined in this file. Using other options of force field also gives error at some point. waiting for your suggestion to proceed further. One of the most important choices when conducting MD simulations is the force field. You'll have to find one that works. It appears that (unfortunately) the Gromos force fields do not work out of the box when heme is involved. If you want specific advice about other force fields, you'll have to describe your problem much better than gives error at some point. No one can help you sort that out. You'd do well to look into the literature. Simulations of heme proteins are not novel, so clearly others have made this work, and in some cases, parameters might be provided for the terms that are missing. -Justin shahid Nayeem On 7/15/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. I was having N-terminal ACE group which I simply deleted from the pdb. Am I right in deleting this group. How should I proceed to get rid of this error. That seems like a particularly poor solution. Simply getting rid of an inconvenient group does not sound appropriate. Ask yourself whether or not there is some functionally significant reason to having the ACE group there (chain truncation? artificial modification?) and decide. As for the errors, look into the topology to see which atoms are causing the problems. Then decide if there are indeed appropriate parameters in the force field for this task. -Justin Thanks in anticipation of help. Shahid Nayeem -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech
[gmx-users] Replica exhange - no. of processors
Hi, I would like to know if the Number_of_processors must be = Number_of_replicas? Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-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
Re: [gmx-users] Replica exhange - no. of processors
No. For GMX4 each replica can be run on multiple processors. Lanyuan On Mon, Jul 19, 2010 at 10:36 AM, Sai Pooja saipo...@gmail.com wrote: Hi, I would like to know if the Number_of_processors must be = Number_of_replicas? Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] Tabulated potentials and performance
Hi, Do you know where can I find some information on how using tabulated potential affects gmx performance, and how? I have to decide how to project a custom model but I don't want to calculate dozens of tables only to find that gmx grinds to a halt. thanks! M. -- gmx-users mailing listgmx-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
Re: [gmx-users] Replica exhange - no. of processors
Thanks Lanyuan. Can one use fewer processors than the number of replicas? Pooja On Mon, Jul 19, 2010 at 12:18 PM, Lanyuan Lu lulanyuan...@gmail.com wrote: No. For GMX4 each replica can be run on multiple processors. Lanyuan On Mon, Jul 19, 2010 at 10:36 AM, Sai Pooja saipo...@gmail.com wrote: Hi, I would like to know if the Number_of_processors must be = Number_of_replicas? Regards Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-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
Re: [gmx-users] Tabulated potentials and performance
It will be very little from my experience. Remember that the dominate part is the non-bonded force calculation. dawei On Mon, Jul 19, 2010 at 12:22 PM, ms deviceran...@gmail.com wrote: Hi, Do you know where can I find some information on how using tabulated potential affects gmx performance, and how? I have to decide how to project a custom model but I don't want to calculate dozens of tables only to find that gmx grinds to a halt. thanks! M. -- gmx-users mailing list gmx-us...@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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Need For a Script
Another thing is that I am not sure how to get the force-extension profile from the simulation trajectory? Thanks Samrat From: Samrat Pal psamra...@yahoo.com To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sun, July 18, 2010 12:21:04 PM Subject: Re: [gmx-users] Need For a Script I have been doing the pull simulations with your scripts and that are running fine. Thanks a lot. Can I use implicit solvent model in pulling simulations? I have gone through the mailing list and I found that it is not recommended (I may be wrong). Please suggest. Thanks in advance Samrat Pal From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a Script Samrat Pal wrote: Dear All, I am a new GROMACS user. I have been able to solvate a protein in a water box and also to simulate it and unfold it by heating it. But I have facing problem with the script of AFM pulling. I want to unfold a protein by pulling the two ends of the protein. Can anyone give me a full script for that so that I can standardise my protocol? Suggestion is urgent. http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling Also, as a bit of advice, don't use the word urgent when asking for free help. You're hoping someone else (who is busy) will find time to solve an issue for you. -Justin Thanks in advance Samrat Pal -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] bond potential selection
Hi all, Could anybody please suggest what potential (from those available in gromacs) would be the best choice to look at the mechanical properties of the polymer/composite? Dr. Vitaly Chaban -- gmx-users mailing listgmx-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
Re: [gmx-users] Tabulated potentials and performance
On 19/07/10 17:32, Da-Wei Li wrote: It will be very little from my experience. Remember that the dominate part is the non-bonded force calculation. Well, that's exactly what I tabulate. dawei On Mon, Jul 19, 2010 at 12:22 PM, msdeviceran...@gmail.com wrote: Hi, Do you know where can I find some information on how using tabulated potential affects gmx performance, and how? I have to decide how to project a custom model but I don't want to calculate dozens of tables only to find that gmx grinds to a halt. thanks! M. -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Tabulated potentials and performance
I remember the manu states that it won't cost too much compared with standard potential function form. dawei On Mon, Jul 19, 2010 at 1:22 PM, ms deviceran...@gmail.com wrote: On 19/07/10 17:32, Da-Wei Li wrote: It will be very little from my experience. Remember that the dominate part is the non-bonded force calculation. Well, that's exactly what I tabulate. dawei On Mon, Jul 19, 2010 at 12:22 PM, msdeviceran...@gmail.com wrote: Hi, Do you know where can I find some information on how using tabulated potential affects gmx performance, and how? I have to decide how to project a custom model but I don't want to calculate dozens of tables only to find that gmx grinds to a halt. thanks! M. -- gmx-users mailing list gmx-us...@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 -- gmx-users mailing list gmx-us...@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 -- gmx-users mailing listgmx-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
[gmx-users] topology for a cyclic peptide
Hi, I am trying to get the topology of a cyclic peptide, but when I try to do pdb2pgx I get automatically the correction to a terminal one. I have looked in the Gromacs list and I only have found a entry about it, http://osdir.com/ml/science.biology.gromacs.user/2006-08/msg00297.html but I cannot find a solution from there. Does anyone have any idea about it, please? Thanks a lot for your help. Best wishes, Rebeca García Santiago de Compostela University Spain _ No has visto nada como el nuevo Messenger, ¡te sorprenderá! http://explore.live.com/windows-live-messenger-- gmx-users mailing listgmx-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
Re: [gmx-users] Tabulated potentials and performance
On 19/07/10 18:32, Da-Wei Li wrote: I remember the manu states that it won't cost too much compared with standard potential function form. Well, I find in the manual exactly the opposite: Note that table lookup is significantly slower than computation of the most simple Lennard-Jones and Coulomb interaction. (p.133) But I am already using tables for most nonbonded interactions and the performance is OK. What I would like to know is, if I increase the *number of tables* (keeping the number of particles/interactions the same, but, say, using two tables where I used only one before), is it going to be significantly worse or not? thanks! m. dawei On Mon, Jul 19, 2010 at 1:22 PM, msdeviceran...@gmail.com wrote: On 19/07/10 17:32, Da-Wei Li wrote: It will be very little from my experience. Remember that the dominate part is the non-bonded force calculation. Well, that's exactly what I tabulate. dawei On Mon, Jul 19, 2010 at 12:22 PM, msdeviceran...@gmail.comwrote: Hi, Do you know where can I find some information on how using tabulated potential affects gmx performance, and how? I have to decide how to project a custom model but I don't want to calculate dozens of tables only to find that gmx grinds to a halt. thanks! M. -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] selenomethionine parameters for ffG53a6
Hi all, Where can I find selenomethionine parameters for ffG53a6 forcefield? Deniz. -- gmx-users mailing listgmx-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
Re: [gmx-users] Tabulated potentials and performance
From our group's experience, there is a critical point for dramatic performance drop when one uses two many tables. The possible reason is that the size of tables exceeds the cache size. However, this only happens when the number of tables is beyond something like 50. The total table size for the critical point can depend on the hardware condition. Lanyuan On Mon, Jul 19, 2010 at 1:49 PM, ms deviceran...@gmail.com wrote: On 19/07/10 18:32, Da-Wei Li wrote: I remember the manu states that it won't cost too much compared with standard potential function form. Well, I find in the manual exactly the opposite: Note that table lookup is significantly slower than computation of the most simple Lennard-Jones and Coulomb interaction. (p.133) But I am already using tables for most nonbonded interactions and the performance is OK. What I would like to know is, if I increase the *number of tables* (keeping the number of particles/interactions the same, but, say, using two tables where I used only one before), is it going to be significantly worse or not? thanks! m. dawei On Mon, Jul 19, 2010 at 1:22 PM, msdeviceran...@gmail.com wrote: On 19/07/10 17:32, Da-Wei Li wrote: It will be very little from my experience. Remember that the dominate part is the non-bonded force calculation. Well, that's exactly what I tabulate. dawei On Mon, Jul 19, 2010 at 12:22 PM, msdeviceran...@gmail.comwrote: Hi, Do you know where can I find some information on how using tabulated potential affects gmx performance, and how? I have to decide how to project a custom model but I don't want to calculate dozens of tables only to find that gmx grinds to a halt. thanks! M. -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] Heme_Grompp Error
Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.01e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) --- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of heme porphyrins. It is actually these six bond which is created in topology file with pdb2gmx using specbond.dat, giving error in grompp. I tried to find these bonds in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem -- gmx-users mailing listgmx-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
