[gmx-users] Linear Interaction Energy Calculation (LIE) using gromacs
Dear all, I want to perform LIE calculations. I want to know what are the steps for LIE calculations. I know that we need to perform two simulations for Protein-Ligand and Ligand separately. Are these two simulations are same as we do in regular MD simulations with EM->NVT->NPT->Prod-RUN steps? What are things to consider while performing LIE? Thanks Bhupendra -- 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.
[gmx-users] Linear Interaction Energy Calculation (LIE) using gromacs
Dear all, I want to perform LIE calculations. I want to know what are the steps for LIE calculations. I know that we need to perform two simulations for Protein-Ligand and Ligand separately. Are these two simulations are same as we do in regular MD simulations with EM->NVT->NPT->Prod-RUN steps? What are things to consider while performing LIE? Thanks Bhupendra -- 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.
Re: [gmx-users] Fw: problem in extending MD in Gromacs 2018
hi I saw Gromacs documentary about how to extend MD run but when I used these two commands: gmx convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr gmx mdrun -s next.tpr -cpi state.cpt my MD run start from the first step. I used these command before without any problem and I wondered what is happen in Gromacs 2018 version. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Tuesday, October 30, 2018 6:37:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fw: problem in extending MD in Gromacs 2018 Hi, We can't tell on the information given, because it is how you call mdrun that matters, but the 2018 log file will tell you what is wrong. For example, if you use gmx mdrun -deffnm md-extended then the output filenames all have different names, and it can't know for sure what you intend. Various operations are no longer supported in more recent versions, because they sometimes led to people losing their files. See also http://manual.gromacs.org/documentation/2018/user-guide/managing-simulations.html#extending-a-tpr-file More generally, the practice of manually naming all your files with numerical suffixes doesn't give you any value. mdrun will do that for you with the -noappend option. Or leave the names as default and restarts and appending will just work. Mark On Tue, Oct 30, 2018 at 3:14 PM Ladan Mafakhe wrote: > > > > > From: Ladan Mafakhe > Sent: Friday, October 19, 2018 11:17 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: problem in extending MD in Gromacs 2018 > > Hello > I use Gromacs 2018 and I have a problem at Extending my MD in this > version. I used these commands for extending my MD: > gmx convert-tpr -s md_0_1.tpr -f md_0_1.trr -e md_0_1.edr -o md-ex.tpr > -until 4 > or > gmx convert-tpr -s md_0_1.tpr -o md-extended.tpr -extend 3 > but in both cases, my MD started at beginning steps and not be extended. > While I did not have such problem in Gromacs 5. What is my problem and how > I can fix it? > I really thank you for helping me with this issue. > Best regards > -- > 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. > -- 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. -- 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.
Re: [gmx-users] ACPYPE not working.
Please, post here the command you're using (add -d anyway for debug) and show the whole output. Thanks, Alan On Thu, 1 Nov 2018 at 20:04, neelam wafa wrote: > Yes it the same one. And the tests are running okay. Problem is with my > files. > > On Fri, 2 Nov 2018, 12:56 am Alan > > Indeed, it worked, though the warning is important. Are you using the > > latest ACPYPE? > > > > > > > > > | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC > (c) > > 2018 AWSdS | > > > > > > > > > > > On Thu, 1 Nov 2018 at 19:46, neelam wafa wrote: > > > > > Means this file worked well on your system? > > > > > > On Fri, 2 Nov 2018, 12:38 am Alan > > > > > > This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try > to > > > get > > > > help at AMBER mailing list. > > > > > > > > For an example I was given, running here: > > > > acpype -di H16.mol2 -c gas > > > > > > > > DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 > -fi > > > > mol2 -o tmp -fo ac -pf y > > > > DEBUG: > > > > Warning: the assigned bond types may be wrong, please : > > > > (1) double check the structure (the connectivity) and/or > > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > > > Be cautious, use a large value of PSCUTOFF (>100) will > > significantly > > > > increase the computation time > > > > > > > > > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa > > wrote: > > > > > > > > > Hi! > > > > > Dear all > > > > > I am using acpype to generate topologies of ligand for gromacs md > > > > > simmulation. I habe amber tools 18 and downloaded acpype from > github. > > > The > > > > > test runs go well but when i run my file with ../acpype.py -i > > UNL.mol2 > > > > -c > > > > > gas or even > > > > > ../acpype.py -di UNL.mol2 > > > > > iI get following error > > > > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal > > > Error! > > > > > Weird atomic valence (2) for atom (ID: 1, Name: C). > > > > >Possible open valence. > > > > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > > > > File "../acpype.py", line 3704, in > > > > > File "../acpype.py", line 3392, in __init__ > > > > > File "../acpype.py", line 910, in setResNameCheckCoords > > > > > Total time of execution: less than a second > > > > > Please any way to get out of this problem? Looking forward for > your > > > > > cooperation > > > > > Regards > > > > > -- > > > > > 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. > > > > > > > > > > > > > > > > > -- > > > > *I** have just cycled* from Land's End to John O'Groats (the > > > > whole Britain!) > > > > for a charity, would you consider supporting my cause? > > > > http://uk.virginmoneygiving.com/AlanSilva > > > > -- > > > > Alan Wilter SOUSA da SILVA, DSc > > > > Senior Bioinformatician, UniProt > > > > European Bioinformatics Institute (EMBL-EBI) > > > > European Molecular Biology Laboratory > > > > Wellcome Trust Genome Campus > > > > Hinxton > > > > Cambridge CB10 1SD > > > > United Kingdom > > > > Tel: +44 (0)1223 494588 > > > > -- > > > > 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. > > > -- > > > 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. > > > > > > > > -- > > *I** have just cycled* from Land's End to John O'Groats (the > > whole Britain!) > > for a charity, would you consider supporting my cause? > > http://uk.virginmoneygiving.com/AlanSilva > > -- > > Alan Wilter SOUSA da SILVA, DSc > > Senior Bioinformatician, UniProt > > European Bioinformatics Institute (EMBL-EBI) > > European Molecular Biology Laboratory > > Wellcome
Re: [gmx-users] Crystal Simulation
Here is an example for bulk molybdenum disulfide. These directives go into atomname2type.n2t in your forcefield directory (I usually have a stand-alone directory in the local simulation folder): MO opls_2000 0.5 95.940 6 S 0.237 S 0.237 S 0.237 S 0.237 S 0.237 S 0.237 ;bulk MO S opls_2004 -0.25 32.065 3 MO 0.237 MO 0.237 MO 0.237 ;bulk S The concept is very simple: the leftmost entry is the label, then the opls type you've given it throughout the forcefield, then charge, then mass, then the number of bonds it participates in, then the list of constituents in those bonds with corresponding distances. x2top uses those distances with a 10% tolerance to set types in the corresponding topologies. In other words, MO atom has a type opls_2000, a charge of +0.5, a mass of such and such, has a total of six nearest neighbors of the type S, each residing at the distance of 0.237 nm. Those neighbors can all be different with different bond lengths, etc. The only thing left to do after this is set up your bonded and nonbonded parameters for these types and off you go. Note that the charge and the mass present in the atomname2type will override the values on ffnonbonded.itp. Definitely the case for the charge (I never really had different masses set in the two directives). Hope this helps. Alex On Thu, Nov 1, 2018 at 3:18 PM tca1 wrote: > In that case it sounds like gmx x2top is what I need, but reading > about it online suggests I also need some kind of residue entry for > the crystal itself. I'm not clear what this entry needs to include in > order to work properly with x2top for a periodic crystal, so do you > have some specific .rtp and .top files I could look at for an example > system to see how you set this up? > > Thanks, > Tom > > > Message: 1 > > Date: Wed, 31 Oct 2018 18:25:34 -0600 > > From: Alex > > To: Discussion list for GROMACS users > > Cc: Discussion list for GROMACS users > > > > Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue > > 87 > > Message-ID: > > < > camjz6qf2osiujve8kscma3ntovk_whq8hlbhkn2jipqte8n...@mail.gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > The connectivity is set at the topology creation stage, which is separate > > from the mdp option "periodic-molecules." As long as the box size is > > commensurate with the crystal and the edges are properly periodic, gmx > > x2top used with proper options will create connectivity across the box > > without any trouble. We use it routinely on crystal structures and it > works > > fine. > > > > Alex > > > > On Wed, Oct 31, 2018 at 5:46 PM tca1 wrote: > > > >> The forces and parameters aren't a problem, that's all been developed > >> separately. My main concern is the connectivity of the crystal surface > >> itself with periodic images. Is there a way to explicitly denote a > >> connection between atoms in the box and their periodic images, or do I > >> just have to play with the box sizes and hope for the best? > >> > >> I did see something about the periodic-molecules option while > >> searching through the manual and online for this topic, but I can't > >> find much detail about proper usage or if it's even relevant to what > >> I'm working with here. Really any clarification on how to properly > >> represent simple 2D crystal structures in simulations with GROMACS > >> would be a great help; maybe this is covered in the papers you linked > >> or associated SI, I can take a look there first. > >> > >> -Tom > >> > >> > Message: 3 > >> > Date: Wed, 31 Oct 2018 16:24:01 -0600 > >> > From: Alex > >> > To: Discussion list for GROMACS users > >> > Cc: Discussion list for GROMACS users > >> > > >> > Subject: Re: [gmx-users] Crystal Surfaces in GROMACS > >> > Message-ID: > >> >>> jxn-isdtdln2lcgxvbwnfcfdk...@mail.gmail.com> > >> > Content-Type: text/plain; charset="UTF-8" > >> > > >> > Hi, > >> > > >> > There are two main reasons there aren't any serious tutorials: first, > >> > Gromacs wasn't originally intended for this type of simulations and > >> second, > >> > it's not clear what such a tutorial would describe. If you have a > >> suitable > >> > interaction model for the material you'd like to simulate, the "usual" > >> > rules (box dimensions commensurate with PBC for a given crystal > >> structure, > >> > careful relaxation procedures, thermostat/barostat considerations, > etc) > >> of > >> > solid-state simulations apply, i.e. there isn't anything terribly > >> specific > >> > to representing any such systems in Gromacs, given that it remains a > very > >> > well designed general MD tool to work with non-reactive systems. We've > >> used > >> > Gromacs to simulate 2D materials in aqueous environment, maybe they > could > >> > be helpful: > >> > > >> > https://pubs.rsc.org/en/content/articlehtml/2016/nr/c5nr07061a > >> > https://pubs.acs.org/doi/abs/10.1021/acsnano.6b05274 > >> > https://pubs.acs.org/doi/abs/10.1021/acsnano.8b01692 > >> >
Re: [gmx-users] Turn on/off residues in gromacs
Dear Justin, Could you please give me comments about the Mimicking nascent peptide elongation part in the Materials and Methods section of this paper: https://www.nature.com/articles/s41598-018-24344-9 Thank you so much -- 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.
Re: [gmx-users] Crystal Simulation
In that case it sounds like gmx x2top is what I need, but reading about it online suggests I also need some kind of residue entry for the crystal itself. I'm not clear what this entry needs to include in order to work properly with x2top for a periodic crystal, so do you have some specific .rtp and .top files I could look at for an example system to see how you set this up? Thanks, Tom Message: 1 Date: Wed, 31 Oct 2018 18:25:34 -0600 From: Alex To: Discussion list for GROMACS users Cc: Discussion list for GROMACS users Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 174, Issue 87 Message-ID: Content-Type: text/plain; charset="UTF-8" The connectivity is set at the topology creation stage, which is separate from the mdp option "periodic-molecules." As long as the box size is commensurate with the crystal and the edges are properly periodic, gmx x2top used with proper options will create connectivity across the box without any trouble. We use it routinely on crystal structures and it works fine. Alex On Wed, Oct 31, 2018 at 5:46 PM tca1 wrote: The forces and parameters aren't a problem, that's all been developed separately. My main concern is the connectivity of the crystal surface itself with periodic images. Is there a way to explicitly denote a connection between atoms in the box and their periodic images, or do I just have to play with the box sizes and hope for the best? I did see something about the periodic-molecules option while searching through the manual and online for this topic, but I can't find much detail about proper usage or if it's even relevant to what I'm working with here. Really any clarification on how to properly represent simple 2D crystal structures in simulations with GROMACS would be a great help; maybe this is covered in the papers you linked or associated SI, I can take a look there first. -Tom > Message: 3 > Date: Wed, 31 Oct 2018 16:24:01 -0600 > From: Alex > To: Discussion list for GROMACS users > Cc: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Crystal Surfaces in GROMACS > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Hi, > > There are two main reasons there aren't any serious tutorials: first, > Gromacs wasn't originally intended for this type of simulations and second, > it's not clear what such a tutorial would describe. If you have a suitable > interaction model for the material you'd like to simulate, the "usual" > rules (box dimensions commensurate with PBC for a given crystal structure, > careful relaxation procedures, thermostat/barostat considerations, etc) of > solid-state simulations apply, i.e. there isn't anything terribly specific > to representing any such systems in Gromacs, given that it remains a very > well designed general MD tool to work with non-reactive systems. We've used > Gromacs to simulate 2D materials in aqueous environment, maybe they could > be helpful: > > https://pubs.rsc.org/en/content/articlehtml/2016/nr/c5nr07061a > https://pubs.acs.org/doi/abs/10.1021/acsnano.6b05274 > https://pubs.acs.org/doi/abs/10.1021/acsnano.8b01692 > > For polymers, it would similarly hinge on the existence of a forcefield and > if it doesn't exist, well, you will have to develop it. ;) If the processes > of interest involve reactive forcefields (i.e. covalent bonds get broken > and created), then you need another MD package, e.g., LAMMPS. > > Hope this helps. > > Alex > > On Wed, Oct 31, 2018 at 2:42 PM tca1 wrote: > >> I've been trying to find out if there are any tutorials on simulating >> crystals (specifically crystal surfaces) using GROMACS; most of the >> tutorials I can find online seem to focus on finite-sized biomolecules >> and I don't know how the topology and run parameters would change with >> periodic surfaces. >> >> For context, I'm interested in studying some aspects of polymer >> behavior at solvent-surface interfaces, and a 2D crytalline surface >> seems like the most direct way to model this, but if there's a >> different way of representing such interfaces in GROMACS, I'd also be >> interested in pursuing that approach. >> >> Thanks, >> Thomas Allen >> >> >> -- >> 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. >> > > > -- > > -- > 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
Re: [gmx-users] NPT not working
On 11/1/18 7:33 AM, Hanin Omar wrote: Dear all gromacs user; I am new to gromacs, and i desperatly need help. I want to use gromacs to calculate the internal dynamics trajectory within a protein. For my simulation i followed this protocol: 1)Use pdb2gmx to generate the gro file and topology ( i chose amber99SB and TIP3P water modrel) 2)Energy minimization in vacuum 3) set perodic boundery coditions 4)solvate the system 5) ADD ions to neutralize the system 6)Energy minimization of the solvated system 7) Position restrainted MD 8)Unrestraind MD ( NVT equiliberation) 9)Unrestraind MD ( NPT equiliberation) 10)Run MD simulation with the addition of RDC restraint in the topology like this ; Include Position restraint file #ifdef POSRES #include "RDC-restraint.itp" #endif The problem is i always get the following eroor when i run the last step (Fatal error: Error: Too many iterations in routine JACOBI) I researched the error and some suggested that the system wasnt equiliberated enough, after checking it seems that the NPT part doesn't converge, i tried extending the time but that didnt solve it, i tired doing it in two steps: 1st NPT with thermostat = v - rescale and barostat = Berendsen for say 6.5 ps and then run 2ND NPT with thermostat = Nose-Hooover and barostat = Parinello -Rahman for 6.5 ps.But that also didnt help. can someone explain why is this happening( and if it has to do with the RDC constraints)? and how can i solve it? If the introduction of RDC restraints causes a failure, then either (1) the implementation of the restraints is incorrect or (2) your structure is incompatible with those restraints, leading to the buildup of forces and a crash. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] Gmx distance
On 11/1/18 2:25 PM, rose rahmani wrote:
I don't know how? I mean x,y,z(s1, s2,s3) in dist.xvg can easily be
multiplied by (-), but how should i modify second column,i don't know how
s0 is calculated by g_distance to modify it??
The output of -oall is a single value, the actual distance, which I
assume is what you are talking about in your previous message. You can
parse that column in any scripting language you like and
[ pseudocode, not functional ]
if (value < 0)
{
value *= -1
}
-Justin
On Wed, 31 Oct 2018, 19:38 Justin Lemkul, wrote:
On 10/31/18 12:06 PM, rose rahmani wrote:
Hi,
I want to calculate distances between fixed tube in the middle of the box
and amino acids(all are same type)around it. But gmx distance gives me
the
relative distance i mean AA can be front or back( can be 0.5 or -0.5 from
tube) of tube but still |-0.5|=0.5 nm far from it. How can i have the
absolute value of distances?
Would you please help me?
Write a simple post-processing script that multiplies any negative value
by -1.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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posting!
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send a mail to gmx-users-requ...@gromacs.org.
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ACPYPE not working.
Yes it the same one. And the tests are running okay. Problem is with my files. On Fri, 2 Nov 2018, 12:56 am Alan Indeed, it worked, though the warning is important. Are you using the > latest ACPYPE? > > > > | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c) > 2018 AWSdS | > > > > > On Thu, 1 Nov 2018 at 19:46, neelam wafa wrote: > > > Means this file worked well on your system? > > > > On Fri, 2 Nov 2018, 12:38 am Alan > > > > This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to > > get > > > help at AMBER mailing list. > > > > > > For an example I was given, running here: > > > acpype -di H16.mol2 -c gas > > > > > > DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi > > > mol2 -o tmp -fo ac -pf y > > > DEBUG: > > > Warning: the assigned bond types may be wrong, please : > > > (1) double check the structure (the connectivity) and/or > > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > > Be cautious, use a large value of PSCUTOFF (>100) will > significantly > > > increase the computation time > > > > > > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa > wrote: > > > > > > > Hi! > > > > Dear all > > > > I am using acpype to generate topologies of ligand for gromacs md > > > > simmulation. I habe amber tools 18 and downloaded acpype from github. > > The > > > > test runs go well but when i run my file with ../acpype.py -i > UNL.mol2 > > > -c > > > > gas or even > > > > ../acpype.py -di UNL.mol2 > > > > iI get following error > > > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal > > Error! > > > > Weird atomic valence (2) for atom (ID: 1, Name: C). > > > >Possible open valence. > > > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > > > File "../acpype.py", line 3704, in > > > > File "../acpype.py", line 3392, in __init__ > > > > File "../acpype.py", line 910, in setResNameCheckCoords > > > > Total time of execution: less than a second > > > > Please any way to get out of this problem? Looking forward for your > > > > cooperation > > > > Regards > > > > -- > > > > 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. > > > > > > > > > > > > > -- > > > *I** have just cycled* from Land's End to John O'Groats (the > > > whole Britain!) > > > for a charity, would you consider supporting my cause? > > > http://uk.virginmoneygiving.com/AlanSilva > > > -- > > > Alan Wilter SOUSA da SILVA, DSc > > > Senior Bioinformatician, UniProt > > > European Bioinformatics Institute (EMBL-EBI) > > > European Molecular Biology Laboratory > > > Wellcome Trust Genome Campus > > > Hinxton > > > Cambridge CB10 1SD > > > United Kingdom > > > Tel: +44 (0)1223 494588 > > > -- > > > 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. > > -- > > 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. > > > > -- > *I** have just cycled* from Land's End to John O'Groats (the > whole Britain!) > for a charity, would you consider supporting my cause? > http://uk.virginmoneygiving.com/AlanSilva > -- > Alan Wilter SOUSA da SILVA, DSc > Senior Bioinformatician, UniProt > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Tel: +44 (0)1223 494588 > -- > 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
Re: [gmx-users] ACPYPE not working.
Indeed, it worked, though the warning is important. Are you using the latest ACPYPE? | ACPYPE: AnteChamber PYthon Parser interfacE v. 2018-09-20T16:44:17UTC (c) 2018 AWSdS | On Thu, 1 Nov 2018 at 19:46, neelam wafa wrote: > Means this file worked well on your system? > > On Fri, 2 Nov 2018, 12:38 am Alan > > This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to > get > > help at AMBER mailing list. > > > > For an example I was given, running here: > > acpype -di H16.mol2 -c gas > > > > DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi > > mol2 -o tmp -fo ac -pf y > > DEBUG: > > Warning: the assigned bond types may be wrong, please : > > (1) double check the structure (the connectivity) and/or > > (2) adjust atom valence penalty parameters in APS.DAT, and/or > > (3) increase PSCUTOFF in define.h and recompile bondtype.c > > Be cautious, use a large value of PSCUTOFF (>100) will significantly > > increase the computation time > > > > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa wrote: > > > > > Hi! > > > Dear all > > > I am using acpype to generate topologies of ligand for gromacs md > > > simmulation. I habe amber tools 18 and downloaded acpype from github. > The > > > test runs go well but when i run my file with ../acpype.py -i UNL.mol2 > > -c > > > gas or even > > > ../acpype.py -di UNL.mol2 > > > iI get following error > > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal > Error! > > > Weird atomic valence (2) for atom (ID: 1, Name: C). > > >Possible open valence. > > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > > File "../acpype.py", line 3704, in > > > File "../acpype.py", line 3392, in __init__ > > > File "../acpype.py", line 910, in setResNameCheckCoords > > > Total time of execution: less than a second > > > Please any way to get out of this problem? Looking forward for your > > > cooperation > > > Regards > > > -- > > > 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. > > > > > > > > > -- > > *I** have just cycled* from Land's End to John O'Groats (the > > whole Britain!) > > for a charity, would you consider supporting my cause? > > http://uk.virginmoneygiving.com/AlanSilva > > -- > > Alan Wilter SOUSA da SILVA, DSc > > Senior Bioinformatician, UniProt > > European Bioinformatics Institute (EMBL-EBI) > > European Molecular Biology Laboratory > > Wellcome Trust Genome Campus > > Hinxton > > Cambridge CB10 1SD > > United Kingdom > > Tel: +44 (0)1223 494588 > > -- > > 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. > -- > 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. -- *I** have just cycled* from Land's End to John O'Groats (the whole Britain!) for a charity, would you consider supporting my cause? http://uk.virginmoneygiving.com/AlanSilva -- Alan Wilter SOUSA da SILVA, DSc Senior Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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.
Re: [gmx-users] ACPYPE not working.
Means this file worked well on your system? On Fri, 2 Nov 2018, 12:38 am Alan This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to get > help at AMBER mailing list. > > For an example I was given, running here: > acpype -di H16.mol2 -c gas > > DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi > mol2 -o tmp -fo ac -pf y > DEBUG: > Warning: the assigned bond types may be wrong, please : > (1) double check the structure (the connectivity) and/or > (2) adjust atom valence penalty parameters in APS.DAT, and/or > (3) increase PSCUTOFF in define.h and recompile bondtype.c > Be cautious, use a large value of PSCUTOFF (>100) will significantly > increase the computation time > > > On Thu, 1 Nov 2018 at 08:53, neelam wafa wrote: > > > Hi! > > Dear all > > I am using acpype to generate topologies of ligand for gromacs md > > simmulation. I habe amber tools 18 and downloaded acpype from github. The > > test runs go well but when i run my file with ../acpype.py -i UNL.mol2 > -c > > gas or even > > ../acpype.py -di UNL.mol2 > > iI get following error > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > > Weird atomic valence (2) for atom (ID: 1, Name: C). > >Possible open valence. > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > File "../acpype.py", line 3704, in > > File "../acpype.py", line 3392, in __init__ > > File "../acpype.py", line 910, in setResNameCheckCoords > > Total time of execution: less than a second > > Please any way to get out of this problem? Looking forward for your > > cooperation > > Regards > > -- > > 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. > > > > > -- > *I** have just cycled* from Land's End to John O'Groats (the > whole Britain!) > for a charity, would you consider supporting my cause? > http://uk.virginmoneygiving.com/AlanSilva > -- > Alan Wilter SOUSA da SILVA, DSc > Senior Bioinformatician, UniProt > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > Tel: +44 (0)1223 494588 > -- > 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. -- 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.
Re: [gmx-users] ACPYPE not working.
This kind of problem is due to ANTECHAMBER, not ACPYPE. You may try to get help at AMBER mailing list. For an example I was given, running here: acpype -di H16.mol2 -c gas DEBUG: /Users/alan/Programmes/amber16/bin/*antechamber* -i H16.mol2 -fi mol2 -o tmp -fo ac -pf y DEBUG: Warning: the assigned bond types may be wrong, please : (1) double check the structure (the connectivity) and/or (2) adjust atom valence penalty parameters in APS.DAT, and/or (3) increase PSCUTOFF in define.h and recompile bondtype.c Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time On Thu, 1 Nov 2018 at 08:53, neelam wafa wrote: > Hi! > Dear all > I am using acpype to generate topologies of ligand for gromacs md > simmulation. I habe amber tools 18 and downloaded acpype from github. The > test runs go well but when i run my file with ../acpype.py -i UNL.mol2 -c > gas or even > ../acpype.py -di UNL.mol2 > iI get following error > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > Weird atomic valence (2) for atom (ID: 1, Name: C). >Possible open valence. > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > File "../acpype.py", line 3704, in > File "../acpype.py", line 3392, in __init__ > File "../acpype.py", line 910, in setResNameCheckCoords > Total time of execution: less than a second > Please any way to get out of this problem? Looking forward for your > cooperation > Regards > -- > 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. > -- *I** have just cycled* from Land's End to John O'Groats (the whole Britain!) for a charity, would you consider supporting my cause? http://uk.virginmoneygiving.com/AlanSilva -- Alan Wilter SOUSA da SILVA, DSc Senior Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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.
Re: [gmx-users] Gmx distance
I don't know how? I mean x,y,z(s1, s2,s3) in dist.xvg can easily be multiplied by (-), but how should i modify second column,i don't know how s0 is calculated by g_distance to modify it?? On Wed, 31 Oct 2018, 19:38 Justin Lemkul, wrote: > > > On 10/31/18 12:06 PM, rose rahmani wrote: > > Hi, > > > > I want to calculate distances between fixed tube in the middle of the box > > and amino acids(all are same type)around it. But gmx distance gives me > the > > relative distance i mean AA can be front or back( can be 0.5 or -0.5 from > > tube) of tube but still |-0.5|=0.5 nm far from it. How can i have the > > absolute value of distances? > > Would you please help me? > > Write a simple post-processing script that multiplies any negative value > by -1. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- 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.
Re: [gmx-users] ACPYPE not working.
Yes i have sourced antechamber and both antechamber -h and acpype -h command work. When i run command acpype.py -i ligand.mol2 It says no such file or directory 'temp' With acpype.py -di ligand.mol2 its gives above error. On Thu, 1 Nov 2018, 4:46 pm Ali Khodayari Have you tried to source amber before commanding acpype for the conversion? > Apparently it’s looking for antechamber but it can’t access it. > When amber is sourced first, you can get a result from commands such as > antechamber -h > Try to first source your amber, and then run acpype. > > > On 1 Nov 2018, at 09:52, neelam wafa wrote: > > > > Hi! > > Dear all > > I am using acpype to generate topologies of ligand for gromacs md > > simmulation. I habe amber tools 18 and downloaded acpype from github. The > > test runs go well but when i run my file with ../acpype.py -i UNL.mol2 > -c > > gas or even > > ../acpype.py -di UNL.mol2 > > iI get following error > > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > > Weird atomic valence (2) for atom (ID: 1, Name: C). > > Possible open valence. > > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > > File "../acpype.py", line 3704, in > > File "../acpype.py", line 3392, in __init__ > > File "../acpype.py", line 910, in setResNameCheckCoords > > Total time of execution: less than a second > > Please any way to get out of this problem? Looking forward for your > > cooperation > > Regards > > -- > > 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. > -- > 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. -- 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.
Re: [gmx-users] ACPYPE not working.
Have you tried to source amber before commanding acpype for the conversion? Apparently it’s looking for antechamber but it can’t access it. When amber is sourced first, you can get a result from commands such as antechamber -h Try to first source your amber, and then run acpype. > On 1 Nov 2018, at 09:52, neelam wafa wrote: > > Hi! > Dear all > I am using acpype to generate topologies of ligand for gromacs md > simmulation. I habe amber tools 18 and downloaded acpype from github. The > test runs go well but when i run my file with ../acpype.py -i UNL.mol2 -c > gas or even > ../acpype.py -di UNL.mol2 > iI get following error > /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! > Weird atomic valence (2) for atom (ID: 1, Name: C). > Possible open valence. > ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' > File "../acpype.py", line 3704, in > File "../acpype.py", line 3392, in __init__ > File "../acpype.py", line 910, in setResNameCheckCoords > Total time of execution: less than a second > Please any way to get out of this problem? Looking forward for your > cooperation > Regards > -- > 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. -- 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.
[gmx-users] NPT not working
Dear all gromacs user; I am new to gromacs, and i desperatly need help. I want to use gromacs to calculate the internal dynamics trajectory within a protein. For my simulation i followed this protocol: 1)Use pdb2gmx to generate the gro file and topology ( i chose amber99SB and TIP3P water modrel) 2)Energy minimization in vacuum 3) set perodic boundery coditions 4)solvate the system 5) ADD ions to neutralize the system 6)Energy minimization of the solvated system 7) Position restrainted MD 8)Unrestraind MD ( NVT equiliberation) 9)Unrestraind MD ( NPT equiliberation) 10)Run MD simulation with the addition of RDC restraint in the topology like this ; Include Position restraint file #ifdef POSRES #include "RDC-restraint.itp" #endif The problem is i always get the following eroor when i run the last step (Fatal error: Error: Too many iterations in routine JACOBI) I researched the error and some suggested that the system wasnt equiliberated enough, after checking it seems that the NPT part doesn't converge, i tried extending the time but that didnt solve it, i tired doing it in two steps: 1st NPT with thermostat = v - rescale and barostat = Berendsen for say 6.5 ps and then run 2ND NPT with thermostat = Nose-Hooover and barostat = Parinello -Rahman for 6.5 ps.But that also didnt help. can someone explain why is this happening( and if it has to do with the RDC constraints)? and how can i solve it? THank you Hanin Omar Sent from my iPhone -- 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.
[gmx-users] Parameter generation for covalently bonded ligands
Dear all, I want to make two covalent bonds between ligands and two bases of DNA . For this I want to generate amber parameters of covalently bonded ligands for running in Gromacs. In normal case without co-valent bonds we are able to generate parameters. but for two co-valentely bonded bases we are unable. We have found some tutorials for normal one but not for two covalently bonded one. If some one have any idea then hoping response from his side. -- *With Best-Rakesh Kumar Mishra* * (RA)CSD SINP Kolkata, India* *E-mail - rakesh.mis...@saha.ac.in * *Phone n. +91 9473662491, +918777496532* -- 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.
[gmx-users] ACPYPE not working.
Hi! Dear all I am using acpype to generate topologies of ligand for gromacs md simmulation. I habe amber tools 18 and downloaded acpype from github. The test runs go well but when i run my file with ../acpype.py -i UNL.mol2 -c gas or even ../acpype.py -di UNL.mol2 iI get following error /home/dr/Downloads/amber18/bin/to_be_dispatched/antechamber: Fatal Error! Weird atomic valence (2) for atom (ID: 1, Name: C). Possible open valence. ACPYPE FAILED: [Errno 2] No such file or directory: 'tmp' File "../acpype.py", line 3704, in File "../acpype.py", line 3392, in __init__ File "../acpype.py", line 910, in setResNameCheckCoords Total time of execution: less than a second Please any way to get out of this problem? Looking forward for your cooperation Regards -- 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.
[gmx-users] acpype is not working
Dear all I am trying to convert .oFF and .FRCMOD format files to the format that is compatible with GMX format, so I installed anaconda to use conda install -c acpype -c openbabel -c ambermd command because I did not install amber and openbabel programs. then issued this command: conda install -c acpype -c openbabel -c ambermd python=3.7 and the system replied: solving environment: done All requested packages already installed. But now when I issue the command: "acpype -h or antechamber -h" in the terminal, face to this error: acpype: command not found antechamber: command not found Is there anyone who can help me to solve the problem? I would be appreciated it if anyone can help me. Thanks in advance Farial -- 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.
