Re: [gmx-users] Error in itp file

2017-08-04 Thread Souvik Dey
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

Re: [gmx-users] Error in itp file

2017-08-03 Thread Justin Lemkul
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]

Re: [gmx-users] Error in itp file

2017-08-03 Thread Mohammad Zahidul Hossain Khan
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

Re: [gmx-users] Error in itp file

2017-08-03 Thread Mohammad Zahidul Hossain Khan
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

Re: [gmx-users] Error in itp file

2017-08-03 Thread Souvik Dey
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: > >>

Re: [gmx-users] Error in itp file

2017-08-02 Thread Justin Lemkul
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

Re: [gmx-users] Error in itp file

2017-08-02 Thread Mohammad Zahidul Hossain Khan
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 >

[gmx-users] Error in itp file

2017-08-02 Thread Souvik Dey
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