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 <jalem...@vt.edu> 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 <souvik.de...@gmail.com> 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 <jalem...@vt.edu> 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.