[gmx-users] two ligand itp file from ACPYPE

[Justin Lemkul]

On 2/19/14, 9:34 AM, SEMRAN İPEK wrote:
> Dear Users;
>
> Iwould like to run MD calculations using gromacs 4.6.5. My topology file
> has two ligand. The itp files for these ligands have been generated using
> *ACPYPE.*
> *I have followed the instructions given below to  include
> these separate itp files to the topology file. For instance, atomtypes.itp
> file includes only common atomtypes for two ligands. ligan1.itp and
> ligand2.itp files have their own parameters and starts with *
>
> *[ moleculetype ] directives.*
> *BTW, the conf.gro file has been modified to reflect the changes in
> topology file. Conf.gro file exactly follows the same atom order as in the
> case of topology file.*
> *When I try to run;*
> *editconf_d -f conf.gro  -o newbox.gro -bt dodecahedron -d 1.0, **it gives
> an error like this:*
>
>   Invalid line in conf.gro for atom 1:
> 1 p  C6N    1   0.044   0.083  -0.081
>
>

Without seeing the first few lines of conf.gro, there's nothing to suggest. 
You've likely broken the format somehow.

-Justin

> Presumably, the problem is related to my conf.gro. Could you please shed
> light on this issue? How can I include two ligand of which parameters have
> been gathered from ACPYPE?
>
> *****Instructions****************
> #include "amber99.ff/forcefield.itp"
>
> ; only has [atomtypes]
> #include "my_ligand_atomtypes.itp"
>
> ; these don't introduce [atomtypes] any more
>   #include "ligand1.itp"
> #include "ligand2.itp"
>
> *********************************
>
> Best Regards,
>
> ipek
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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