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
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.
Re: [gmx-users] Error in itp file
write the ligand topology just after the forcefield parameter. ; Include forcefield parameters #include "amber03.ff/forcefield.itp" ; Include ligand topology #include "drg.itp" On Thu, Aug 3, 2017 at 5:53 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. > > 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. -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu * * Skype: parash.khan2* *Cell: +12085967165* -- 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
Can you give web server link? I have tried but didn't find. On Aug 3, 2017 5:53 AM, "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_ > > 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. > -- 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.
Re: [gmx-users] Error in itp file
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.
Re: [gmx-users] Error in itp file
Hi Can you tell me, how have you used ACPYPE for itp. On Aug 2, 2017 9:36 AM, "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? > > 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. > -- 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.