Re: [gmx-users] Non Standard residues moving Away
Hi, Grompp is running successfully without any errors. But my protein and ligands are very far away from each other. So, what I fear is that the interactions among them may not be well accounted for by MD simulations. On Mon, Aug 7, 2017 at 7:53 PM, Mark Abraham wrote: > Hi, > > The only thing that matters is the order of the molecules, residues and > atoms, and preferably naming. These must match between topology and > coordinates when you eg use grompp. The point of doing an MD simulation is > generally to keep the topology constant while changing the coordinates. So > give grompp whatever file in whatever format suits you, subject to the > above constraint. > > Mark > > On Mon, 7 Aug 2017 16:25 Souvik Dey wrote: > > > Hi, > > > > I am trying to simulate a Protein Ligand system. Now, my system has some > > non standard residues and I standardized them for AMBER forcefield using > > ACPYPE. However, when I assemble the gro files of the Proten generated > from > > pdb2gmx and the gro files obtained from ACPYPE, I see that they are not > > situated next to each other. They have have moved far away. > > > > Now, is there any trick by which the coordinates of the PDB file do not > > change while being converted into a gro file or is there any way to > restore > > the previous condition of the PDB file? > > > > Thanking you, > > Souvik Dey > > > > -- > > Souvik Dey > > Integrated Science Education & Research Centre > > Visva Bharati University > > Santiniketan-731235 > > West Bengal > > 8981736643 > > -- > > 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. > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] How to configure the gro/itp/top files after running "insert-molecules"?
But what if the coordinates do not match? I mean Glycine may not have the same coordinates after. On Mon, Aug 7, 2017 at 2:48 PM, yujie liu wrote: > > The .top file of protein has included itself all parameters, so now you > only copy gly.gro into protein.gro and changed the number of atoms. Then > using #include” ” lines to add gly.itp into protein.top in suitable > position and changed [molecules] options to add the name and number of gly > molecule. Note the information of posre_gly.itp. > -- > 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. > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Non Standard residues moving Away
Hi, I am trying to simulate a Protein Ligand system. Now, my system has some non standard residues and I standardized them for AMBER forcefield using ACPYPE. However, when I assemble the gro files of the Proten generated from pdb2gmx and the gro files obtained from ACPYPE, I see that they are not situated next to each other. They have have moved far away. Now, is there any trick by which the coordinates of the PDB file do not change while being converted into a gro file or is there any way to restore the previous condition of the PDB file? Thanking you, Souvik Dey -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Error in itp file
You can use this link for ACPYPE: http://webapps.ccpn.ac.uk/acpype/ First, you have to mail the author and then he would give you a user ID and password. On Fri, Aug 4, 2017 at 1:48 AM, Justin Lemkul wrote: > > > On 8/3/17 8:53 AM, Souvik Dey wrote: > >> Yes, I saw the GROMACS website. But my itp file has [atomtypes] first >> followed by [moleculetypes]. So, I am still not getting what is the >> error. >> >> > All [atomtypes] (and more generally, any force field parameters) must > appear before *any* [moleculetype] directives, not just the one to which > the parameters apply. So a topology that introduces parameters must be > #included before any invocation of a [moleculetype]. > > -Justin > > > On Thu, Aug 3, 2017 at 2:52 PM, Souvik Dey wrote: >> >> Yes, using ACPYPE is pretty simple. They have a web server, where you can >>> upload your PDB or MOL2 file, provide the charge and multiplicity and it >>> gives you the output file. >>> >>> On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul wrote: >>> >>> >>>> >>>> On 8/2/17 12:35 PM, Souvik Dey wrote: >>>> >>>> Hi, >>>>> >>>>> I just generated an itp file from ACPYPE. However, if I try to add ions >>>>> it >>>>> shows the following error: >>>>> >>>>> Fatal error: >>>>> Syntax error - File FAD.itp, line 3 >>>>> Last line read: >>>>> '[ atomtypes ]' >>>>> Invalid order for directive atomtypes >>>>> >>>>> >>>>> Can somebody say how do I fix this? >>>>> >>>>> >>>>> This exact situation is described here: >>>> >>>> http://www.gromacs.org/Documentation/Errors#Invalid_order_fo >>>> r_directive_xxx >>>> >>>> -Justin >>>> >>>> -- >>>> == >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>> >>>> Department of Pharmaceutical Sciences >>>> School of Pharmacy >>>> Health Sciences Facility II, Room 629 >>>> University of Maryland, Baltimore >>>> 20 Penn St. >>>> Baltimore, MD 21201 >>>> >>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>> http://mackerell.umaryland.edu/~jalemkul >>>> >>>> == >>>> >>>> -- >>>> 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. >>>> >>>> >>> >>> >>> -- >>> Souvik Dey >>> Integrated Science Education & Research Centre >>> Visva Bharati University >>> Santiniketan-731235 >>> West Bengal >>> 8981736643 >>> >>> >> >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Error in itp file
Yes, I saw the GROMACS website. But my itp file has [atomtypes] first followed by [moleculetypes]. So, I am still not getting what is the error. On Thu, Aug 3, 2017 at 2:52 PM, Souvik Dey wrote: > Yes, using ACPYPE is pretty simple. They have a web server, where you can > upload your PDB or MOL2 file, provide the charge and multiplicity and it > gives you the output file. > > On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul wrote: > >> >> >> On 8/2/17 12:35 PM, Souvik Dey wrote: >> >>> Hi, >>> >>> I just generated an itp file from ACPYPE. However, if I try to add ions >>> it >>> shows the following error: >>> >>> Fatal error: >>> Syntax error - File FAD.itp, line 3 >>> Last line read: >>> '[ atomtypes ]' >>> Invalid order for directive atomtypes >>> >>> >>> Can somebody say how do I fix this? >>> >>> >> This exact situation is described here: >> >> http://www.gromacs.org/Documentation/Errors#Invalid_order_fo >> r_directive_xxx >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> == >> >> -- >> 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. >> > > > > -- > Souvik Dey > Integrated Science Education & Research Centre > Visva Bharati University > Santiniketan-731235 > West Bengal > 8981736643 > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Error in itp file
Yes, using ACPYPE is pretty simple. They have a web server, where you can upload your PDB or MOL2 file, provide the charge and multiplicity and it gives you the output file. On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul wrote: > > > On 8/2/17 12:35 PM, Souvik Dey wrote: > >> Hi, >> >> I just generated an itp file from ACPYPE. However, if I try to add ions it >> shows the following error: >> >> Fatal error: >> Syntax error - File FAD.itp, line 3 >> Last line read: >> '[ atomtypes ]' >> Invalid order for directive atomtypes >> >> >> Can somebody say how do I fix this? >> >> > This exact situation is described here: > > http://www.gromacs.org/Documentation/Errors#Invalid_order_ > for_directive_xxx > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > > -- > 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. > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Error in itp file
Hi, I just generated an itp file from ACPYPE. However, if I try to add ions it shows the following error: Fatal error: Syntax error - File FAD.itp, line 3 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes Can somebody say how do I fix this? Regards, Souvik Dey -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Error in pdb2gmx
Can you name some of these softwares? I am relatively new in this. On Mon, Jul 31, 2017 at 4:59 PM, Mark Abraham wrote: > Hi, > > You need to build in the residue in a way that makes sense. Using some > other software, but there are some suggestions on the Gromacs website. > > Mark > > On Mon, 31 Jul 2017 16:57 Souvik Dey wrote: > > > Hi, > > > > I am trying to run pdb2gmx on a long Amino Acid chain. However, one of > the > > residues in the middle is incomplete. If I change the residue manually > > myself, would there be any problem in connectivity? Else, how do I sort > out > > this problem? > > > > Souvik > > > > -- > > Souvik Dey > > Integrated Science Education & Research Centre > > Visva Bharati University > > Santiniketan-731235 > > West Bengal > > 8981736643 > > -- > > 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. > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Error in pdb2gmx
Hi, I am trying to run pdb2gmx on a long Amino Acid chain. However, one of the residues in the middle is incomplete. If I change the residue manually myself, would there be any problem in connectivity? Else, how do I sort out this problem? Souvik -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Non Standard Residue in Amber
Hi, I have a non standard residue, FAD, Flavin Adenine Dinucleotide. I need to standardize it for running a simulation using Amber force field. I tried ACPYPE but it is not working for this particular residue. I also read that Parmed can be used for the same purpose, but I could not find how to use it. Also, whenever, I am trying to run Gaussian with FAD, it comes with a convergence error. So, can anyone tell me how do I sort out this issue? Regards, Souvik On Wed, Jul 26, 2017 at 1:07 PM, Souvik Dey wrote: > Hi, > > I have a non standard residue, FAD, Flavin Adenine Dinucleotide. I need to > standardize it for running a simulation using Amber force field. I tried > ACPYPE but it is not working for this particular residue. I also read that > Parmed can be used for the same purpose, but I could not find how to use > it. Also, whenever, I am trying to run Gaussian with FAD, it comes with a > convergence error. > > So, can anyone tell me how do I sort out this issue? > > Regards, > Souvik > > -- > Souvik Dey > Integrated Science Education & Research Centre > Visva Bharati University > Santiniketan-731235 > West Bengal > 8981736643 > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Non Standard Residue in Amber
Hi, I have a non standard residue, FAD, Flavin Adenine Dinucleotide. I need to standardize it for running a simulation using Amber force field. I tried ACPYPE but it is not working for this particular residue. I also read that Parmed can be used for the same purpose, but I could not find how to use it. Also, whenever, I am trying to run Gaussian with FAD, it comes with a convergence error. So, can anyone tell me how do I sort out this issue? Regards, Souvik -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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.
