[gmx-users] N-terminus problem

[Mark Abraham]

On 1/07/2011 8:35 PM, Emine Deniz Tekin wrote:
>
> Hi Gromacs users,
>
>
> I created a lipopeptide (lauroic acid connected to an 8-residue 
> peptide which starts with Valine).
>

How is the link from acid to peptide created?

> ·If I try to use pdb2gmx with -ter flag(Start terminus VAL-2: None, 
> End terminus ASP-9: COO-), everything seems to work (topology is 
> created.).
>

Does that topology work for MD? Why does pdb2gmx think there's 9 
residues, and below there seem to be 63?

> ·But, if I try to use pdb2gmx with -ter flagfor more than one 
> lipopeptide at desired positions, it gives the following error. (again 
> says Start terminus VAL-2: None, End terminus ASP-9: COO- )
>
> *Fatal error:  Atom N not found in residue seq.nr <http://seq.nr>. 1 
> while adding improper*
>
> While I was creating the lipopeptide, I introduced the lauroic acid as 
> a pseudo amino acid (following Mark’s suggestion). So, I really do NOT 
> have atom N in the first residue. I pasted a part of my gro file below.
>

Some improper in your topology database entries wants a N atom that 
doesn't exist. Unfortunately, we don't have anywhere near enough 
information to guess why. pdb2gmx is trying to match your .rtp and 
specbond entries to your .gro file, but only seeing the latter can't 
help diagnose a mismatch. Some description of "desired positions" is 
also important.

Also, giving full command lines are always preferred. You may not think 
anything significant is there, and you might be right, but if there 
*can* be something significant there, and we aren't given the chance to 
know whether it is present, we might just not bother to waste time 
guessing :)

Mark

>
> GROMACS molecule input test
>
> 574
>
> 1DPPCA111.0275.2953.153
>
> 1DPPCB210.8945.2993.078
>
> 1DPPCG310.7775.2343.153
>
> 1DPPCD410.6455.2543.078
>
> 1DPPCE510.5215.2033.153
>
> 1DPPCZ610.3925.2513.086
>
> 1DPPCM710.2665.2073.161
>
> 1DPPCN810.1405.2723.103
>
> 1DPPCO910.0145.2213.172
>
> 1DPPCP109.8855.2793.112
>
> 1DPPCQ119.7615.2033.160
>
> 1DPPC1211.1015.4303.147
>
> 1DPPO1311.0325.5313.136
>
> 2VALN1411.2355.4503.160
>
> 2VALH1511.2495.5503.159
>
> 2VALCA1611.3685.3853.181
>
> 2VALCB1711.3905.2333.181
>
> 2VALCG11811.3325.1723.308
>
> 2VALCG21911.3385.1613.056
>
> 2VALC2011.4865.4493.103
>
> 2VALO2111.4985.4362.982
>
> …………..
>
> 63ASPOD1570-0.30614.8743.343
>
> 63ASPOD2571-0.45115.0303.289
>
> 63ASPC572-0.05715.0233.106
>
> 63ASPO15730.01415.0033.207
>
> 63ASPO2574-0.02915.1043.017
>
> 16.2393716.2393716.23937
>
>
> I am using Gromacs 53a6 force field and gromacs 4.5.3 version.
>
> Any help will be appreciated.
>
> Thanks in advance
>
> Deniz
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110702/12ed86e5/attachment.html>