Re: [gmx-users] Error in pdb2gmx

ons on the Gromacs website. > > Mark > > On Mon, 31 Jul 2017 16:57 Souvik Dey <souvik.de...@gmail.com> 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

[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

Re: [gmx-users] Non Standard Residue in Amber

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 <souvik.de...@gmail.com> wrote: > Hi, > > I have a non standard resid

[gmx-users] Non Standard Residue in Amber

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 898173

[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

Re: [gmx-users] Non Standard residues moving Away

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 <souvik.de...@gmail.com> wrote: > > > Hi, > > > > I am trying to simulate a Pro

[gmx-users] Non Standard residues moving Away

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

Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

sers 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/Maili

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 <jalem...@vt.edu> wrote: > > > On 8/2/17 12:35 PM, Souvik Dey

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 <jalem...@vt.edu> wrote: > > > On 8/3/17 8:53 AM, Souvik Dey wrote: &