sarbani chattopadhyay wrote:
Hi everyone,
I had asked this question before but I will try to
explain myself more clearly.
I wan t to add -NH2 cap at the Cterminal end of my protein. I had
included "charmm" force
field into my gromacs 3.3.1.
I had added the following into my ffcharmm-c.tdb file
[NH2]
[replace]
O OB 15.994 -0.550
CA CT1 12.0110 0.070
C CD 12.0110 0.720
[add]
1 4 NH2 C CA C
NH2 14.0027 -0.7800
I don't know what add type 4 is in the context of a C-terminal database, but in
the .hdb it means to add two or three tetrahedral H atoms.
2 3 HT N CA C
HT 1.0080 0.3100
However, the coordinates of the added N is given by "pdb2gmx" as " nan
nan nan".
Are they present in the input structure? If you're trying to add them through
this mechanism, it probably won't work.
If anyone can give any suggestion to fix this poblem, I will be highly
obliged.
The CHARMM .rtp that I have (from the User Contributions site) contains a
parameterized NH2 residue. That means, if the amide is present in the .pdb file
you have, then all you have to do is give pdb2gmx -ter and select 'None',
instead of messing around with the .tdb files.
-Justin
Thanks in advance,
Sarbani
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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