[gmx-users] peptide lipid simulation

[Justin Lemkul]

Again, please keep the discussion on your list.  I am not your personal tutor.

On 9/24/15 9:48 AM, badamkhatan togoldor wrote:
> Here is my part of .pdb file, looks like this
>
> ATOM      1  H1  POP     1      91.560  89.270  13.210  1.00  0.000
> ATOM      2  H2  POP     1      92.740  89.520  14.390  1.00  0.000
> ATOM      3  H3  POP     1      93.100  89.290  12.880  1.00  0.000
> ATOM      4  N4  POP     1      92.410  89.720  13.470  1.00  0.000
> ATOM      5  C5  POP     1      92.180  91.110  13.060  1.00  0.000
> ATOM      6  C6  POP     1      90.800  90.880  12.440  1.00  0.000
> ATOM      7  O7  POP     1      90.270  89.630  12.890  1.00  0.000
>
> Then I checked merged.rtp file from charmm37.ff,
> So error is in naming convention? or what? I should fix this entire row by POPE ?
>

Indeed, as I said before.

-Justin

> Badamkhatan Tuguldur
>
>
>
> On Thursday, 24 September 2015, 21:28, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> Please be sure to keep the discussion on the mailing list.
>
> On 9/24/15 9:24 AM, badamkhatan togoldor wrote:
>  > Thanks
>  > Oh, charmm37 is working fine. And now on the grompp give me this error.
>  >
>  > Fatal error:
>  > No molecules were defined in the system
>  > For more information and tips for troubleshooting, please check the GROMACS
>  >
>
> Did you visit the URL given in this message?  Most common errors have solutions
> listed here.
>
>  > Is it depending on my peptide.pdb file, there was several kind of pope.pdb
>  > files, so i don't know which one is suitable for me! another pope.pdb file gave
>  > me different error on the pdb2gmx.
>  >
>
> I have no idea what this means.  Several coordinate files?
>
>  > Fatal error:
>  > Residue 'POP' not found in residue topology database
>  >
>  > Any advice?
>  >
>
> "POP" is not a valid residue name.  See the force field .rtp file for valid
> names (spoiler alert: for POPE, the residue name is POPE).
>
> You may want to use CHARMM-GUI to build this system and write its topology if
> you are not familiar with building complex systems.
>
>
> -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
>
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>

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

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

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

==================================================